I have a setup similar to yours (only I use Grub, not Vista's bootloader) and have no problems.
Since Ubuntu and Vista are on separate partitions, they don't "care about each other"; Ubuntu is "just something on the disk" for Vista and vice versa. They shouldn't cause trouble to each other, except for bootloader trouble maybe, but if you can boot both operating systems (at least sometimes), it doesn't sound like that either. Of course you may reinstall your bootloader and see if it helps, but don't expect too much. If I were to guess, I'd say this is just something that got messed up inside Vista and that your easiest/most straight path would be to reinstall Vista completely, see that it works as it should, then reconfigure your bootloader for Ubuntu dual-booting.