Tried to install Ubuntu 12.04 from USB-stick alongside the existing Win7 OS 64bit, and now I'm not sure if install was completely successful: Disk Utility tool claims that the Extended partition (which contains Ubuntu partition and Swap) is "misaligned" and recommends repartition. What should I do, and if should I do this repartition, how to do it (especially if I would like not to lose the data on Win7 partition)?

Background info: A considerably new Thinkpad laptop (UEFI BIOS, if that matters). Before install there were already a "SYSTEM_DRV" partition, the main Windows partition and a Lenovo recovery partition (all NTFS). Now the table looks like this: SYSTEM_DRV (sda1), Windows (sda2), Extended (sda4) (which contains Linux (sda5; ext4) and Swap (sda6)) and Recovery (sda3). Disk Utility Tool gives a message as follows when I select Ext: "The partition is misaligned by 1024 bytes. This may result in very poor performance. Repartitioning is suggested."

There were couple of problems during the install, which I describe below, in the case they happen to be relevant.

Installer claimed that it recognized existing OS'es fine, so I checked the corresponding option during the install. Next, when it asked me how to allocate the disk space, the first weird thing happened: the installer give me a graphical "slide" allocate disk space for pre-existing Win7 OS and new Ubuntu... but it did not inform me which partition would be for Ubuntu and which for Windows. ..well, I decided to go with the setting installer proposed. (not sure if this is relevant, but I guess I'd better mention it anyway - the previous partition tools have been more self-explanatory...)

After the install (which reported no errors), GRUB/Ubuntu refused to boot. Luckily this problem was quite straightforwardly resolved with live-Ubuntu-USB and Boot-Repair ("Recommended repair" worked just fine). After all this hassle I decided to check the partition table "just to be sure"- and the disk utility gives the warning message I described.