A file's "Comments" in OS X are stored in the copy of the invisible ".DS_Store" file that resides in the same folder as the commented file - I believe the change from "Comments" to "Spotlight Comments" is a change in name only. I think many of the problems with comments in "OS X" can be blamed on the "Finder" - like a lot of its other tasks, the "Finder" is lazy and doesn't get around to updating the ".DS_Store" files until it feels like it - maybe there is a reason for this, but I can't think of one. So if a new comment is added, or a file with an old comment is moved and the "Finder" crashes before the ".DS_Store" file is updated, the comments will be lost. In my opinion, this is just bad design - how much sympathy do you have for someone that complains that they lost data because the power went out and they hadn't saved any changes? Unfortunately, this is how the "Finder" treats your data, and not only do you lose changes, but you lose the original as well.
There are a few things that seem to encourage the "Finder" to update the ".DS_Store" files, such as duplicating something in the folder containing the commented item. Another is to "quit" the "Finder" - don't use "Force Quit" or "relaunch" from the "Dock", or '
kill' from the command line - these are the equivalent of crashing the "Finder" in that changes to preferences, etc. aren't saved. Use "Quit" in "Activity Monitor.app", or AppleScript, or enable the Finder's "Quit" menu item to quit. Even "quitting" nicely, sometimes the "Finder" may crash in the process, in which case comments may be lost. Either way, these are just workarounds for the problem that "Finder" doesn't update ".DS_Store" files immediately.
The other problem is that if anything other than "Finder" is used to move a file to a different folder, it is likely that the comments won't be transferred - for example, the unix tools wouldn't have a clue about "comments", and even if they did, I don't think the format of ".DS_Store" files is publicly known so that they could be updated.
If the contents of the comments are important, it would probably be best to either back up frequently, or else don't rely on "Finder" comments to store them. For example, "iPhoto" comments are also stored in a separate file, but the file seems to updated more quickly and more predictably than Finder's ".DS_Store" files.