Take a look at following trace taken with Wireshark:
http://dl.dropbox.com/u/145579/trace1.pcap
or
http://dl.dropbox.com/u/145579/trace2.pcap
I will repeat here an interesting part (from trace1.pcap):
No. Time Source Destination Protocol Length Info
1850 2012-02-09 13:44:32.609 172.22.37.4 192.168.4.213 TCP 54 iso-tsap > 62479 [ACK] Seq=345 Ack=581704 Win=65392 Len=0
1851 2012-02-09 13:44:32.610 192.168.4.213 172.22.37.4 COTP 550 DT TPDU (0) [COTP fragment, 509 bytes]
1852 2012-02-09 13:44:32.639 192.168.4.213 172.22.37.4 COTP 590 DT TPDU (0) [COTP fragment, 509 bytes]
1853 2012-02-09 13:44:32.639 172.22.37.4 192.168.4.213 TCP 54 iso-tsap > 62479 [ACK] Seq=345 Ack=582736 Win=65392 Len=0
1854 2012-02-09 13:44:32.657 192.168.4.213 172.22.37.4 TCP 590 [TCP Previous segment lost] 62479 > iso-tsap [ACK] Seq=583232 Ack=345 Win=65191 Len=536
1855 2012-02-09 13:44:32.657 192.168.4.213 172.22.37.4 TCP 108 [TCP segment of a reassembled PDU]
1856 2012-02-09 13:44:32.657 172.22.37.4 192.168.4.213 TCP 54 [TCP Dup ACK 1853#1] iso-tsap > 62479 [ACK] Seq=345 Ack=582736 Win=65392 Len=0
1857 2012-02-09 13:44:32.657 172.22.37.4 192.168.4.213 TCP 54 [TCP Dup ACK 1853#2] iso-tsap > 62479 [ACK] Seq=345 Ack=582736 Win=65392 Len=0
1858 2012-02-09 13:44:32.675 192.168.4.213 172.22.37.4 COTP 590 [TCP Fast Retransmission] DT TPDU (0) [COTP fragment, 509 bytes]
1859 2012-02-09 13:44:32.715 192.168.4.213 172.22.37.4 TCP 590 [TCP Retransmission] [TCP segment of a reassembled PDU]
1860 2012-02-09 13:44:32.715 172.22.37.4 192.168.4.213 TCP 54 iso-tsap > 62479 [ACK] Seq=345 Ack=583272 Win=65392 Len=0
1861 2012-02-09 13:44:32.796 192.168.4.213 172.22.37.4 COTP 590 [TCP Retransmission] DT TPDU (0) EOT
1862 2012-02-09 13:44:32.945 192.168.4.213 172.22.37.4 TCP 590 [TCP Retransmission] [TCP segment of a reassembled PDU]
1863 2012-02-09 13:44:32.945 172.22.37.4 192.168.4.213 TCP 54 iso-tsap > 62479 [ACK] Seq=345 Ack=583808 Win=65392 Len=0
1864 2012-02-09 13:44:32.963 192.168.4.213 172.22.37.4 COTP 590 DT TPDU (0) [COTP fragment, 509 bytes]
1865 2012-02-09 13:44:32.963 172.22.37.4 192.168.4.213 TCP 54 [TCP Dup ACK 1863#1] iso-tsap > 62479 [ACK] Seq=345 Ack=583808 Win=65392 Len=0
1866 2012-02-09 13:44:32.963 192.168.4.213 172.22.37.4 TCP 576 [TCP segment of a reassembled PDU]
1867 2012-02-09 13:44:32.963 172.22.37.4 192.168.4.213 TCP 54 [TCP Dup ACK 1863#2] iso-tsap > 62479 [ACK] Seq=345 Ack=583808 Win=65392 Len=0
1868 2012-02-09 13:44:33.235 192.168.4.213 172.22.37.4 COTP 590 [TCP Retransmission] DT TPDU (0) [COTP fragment, 509 bytes]
1869 2012-02-09 13:44:33.434 172.22.37.4 192.168.4.213 TCP 54 iso-tsap > 62479 [ACK] Seq=345 Ack=584344 Win=65392 Len=0
1870 2012-02-09 13:44:33.447 192.168.4.213 172.22.37.4 COTP 590 DT TPDU (0) [COTP fragment, 509 bytes]
1871 2012-02-09 13:44:33.447 172.22.37.4 192.168.4.213 TCP 54 [TCP Dup ACK 1869#1] iso-tsap > 62479 [ACK] Seq=345 Ack=584344 Win=65392 Len=0
1872 2012-02-09 13:44:33.806 192.168.4.213 172.22.37.4 COTP 590 [TCP Retransmission] DT TPDU (0) [COTP fragment, 509 bytes]
1873 2012-02-09 13:44:34.006 172.22.37.4 192.168.4.213 TCP 54 iso-tsap > 62479 [ACK] Seq=345 Ack=584880 Win=65392 Len=0
1874 2012-02-09 13:44:34.018 192.168.4.213 172.22.37.4 COTP 590 DT TPDU (0) [COTP fragment, 509 bytes]
1875 2012-02-09 13:44:34.018 172.22.37.4 192.168.4.213 TCP 54 [TCP Dup ACK 1873#1] iso-tsap > 62479 [ACK] Seq=345 Ack=584880 Win=65392 Len=0
1876 2012-02-09 13:44:34.932 192.168.4.213 172.22.37.4 TCP 590 [TCP Retransmission] [TCP segment of a reassembled PDU]
1877 2012-02-09 13:44:35.132 172.22.37.4 192.168.4.213 TCP 54 iso-tsap > 62479 [ACK] Seq=345 Ack=585416 Win=65392 Len=0
1878 2012-02-09 13:44:35.144 192.168.4.213 172.22.37.4 COTP 590 DT TPDU (0) [COTP fragment, 509 bytes]
1879 2012-02-09 13:44:35.144 172.22.37.4 192.168.4.213 TCP 54 [TCP Dup ACK 1877#1] iso-tsap > 62479 [ACK] Seq=345 Ack=585416 Win=65392 Len=0
1880 2012-02-09 13:44:37.172 192.168.4.213 172.22.37.4 TCP 590 [TCP Retransmission] [TCP segment of a reassembled PDU]
1881 2012-02-09 13:44:37.372 172.22.37.4 192.168.4.213 TCP 54 iso-tsap > 62479 [ACK] Seq=345 Ack=585952 Win=65392 Len=0
1882 2012-02-09 13:44:37.385 192.168.4.213 172.22.37.4 COTP 590 DT TPDU (0) [COTP fragment, 509 bytes]
1883 2012-02-09 13:44:37.385 172.22.37.4 192.168.4.213 TCP 54 [TCP Dup ACK 1881#1] iso-tsap > 62479 [ACK] Seq=345 Ack=585952 Win=65392 Len=0
1884 2012-02-09 13:44:41.632 192.168.4.213 172.22.37.4 TCP 590 [TCP Retransmission] [TCP segment of a reassembled PDU]
1885 2012-02-09 13:44:41.832 172.22.37.4 192.168.4.213 TCP 54 iso-tsap > 62479 [ACK] Seq=345 Ack=586488 Win=65392 Len=0
1886 2012-02-09 13:44:41.844 192.168.4.213 172.22.37.4 COTP 590 DT TPDU (0) [COTP fragment, 509 bytes]
1887 2012-02-09 13:44:41.844 172.22.37.4 192.168.4.213 TCP 54 [TCP Dup ACK 1885#1] iso-tsap > 62479 [ACK] Seq=345 Ack=586488 Win=65392 Len=0
1888 2012-02-09 13:44:50.554 192.168.4.213 172.22.37.4 TCP 590 [TCP Retransmission] [TCP segment of a reassembled PDU]
1889 2012-02-09 13:44:50.753 172.22.37.4 192.168.4.213 TCP 54 iso-tsap > 62479 [ACK] Seq=345 Ack=587024 Win=65392 Len=0
1890 2012-02-09 13:44:50.766 192.168.4.213 172.22.37.4 COTP 590 DT TPDU (0) [COTP fragment, 509 bytes]
1891 2012-02-09 13:44:50.766 172.22.37.4 192.168.4.213 TCP 54 [TCP Dup ACK 1889#1] iso-tsap > 62479 [ACK] Seq=345 Ack=587024 Win=65392 Len=0
1892 2012-02-09 13:45:08.385 192.168.4.213 172.22.37.4 TCP 590 [TCP Retransmission] [TCP segment of a reassembled PDU]
1893 2012-02-09 13:45:08.585 172.22.37.4 192.168.4.213 TCP 54 iso-tsap > 62479 [ACK] Seq=345 Ack=587560 Win=65392 Len=0
1894 2012-02-09 13:45:08.598 192.168.4.213 172.22.37.4 COTP 590 DT TPDU (0) [COTP fragment, 509 bytes]
1895 2012-02-09 13:45:08.598 172.22.37.4 192.168.4.213 TCP 54 [TCP Dup ACK 1893#1] iso-tsap > 62479 [ACK] Seq=345 Ack=587560 Win=65392 Len=0
1896 2012-02-09 13:45:44.059 192.168.4.213 172.22.37.4 TCP 590 [TCP Retransmission] [TCP segment of a reassembled PDU]
1897 2012-02-09 13:45:44.259 172.22.37.4 192.168.4.213 TCP 54 iso-tsap > 62479 [ACK] Seq=345 Ack=588096 Win=65392 Len=0
1898 2012-02-09 13:45:44.272 192.168.4.213 172.22.37.4 COTP 590 DT TPDU (0) [COTP fragment, 509 bytes]
1899 2012-02-09 13:45:44.272 172.22.37.4 192.168.4.213 TCP 54 [TCP Dup ACK 1897#1] iso-tsap > 62479 [ACK] Seq=345 Ack=588096 Win=65392 Len=0
1900 2012-02-09 13:46:55.386 192.168.4.213 172.22.37.4 TCP 590 [TCP Retransmission] [TCP segment of a reassembled PDU]
Some background information (not much, unfortunately, as I'm responsible only for server part): Server (172.22.37.4) is Windows Server 2008 R2 and client (192.168.4.213) is Ericsson telephone exchange of whom I do not know much. Client sends a file to server using FTAM protocol. This problem happens very often.
I think, either client or server is doing sliding window protocol wrong. Server sends dup ack, client retransmits lost packet, but soon after client sends packets with wrong seq. Again, Server sends dup ack, client retransmits lost packet - but, this time with longer retransmission timeout. Again, client sends packet with wrong seq. Etc... Retransmission timeout grows to circa 4 minutes and communications never recovers to normal.