I have a similar problem, I have been installing and removing several packages in 10.04, because the installation has several problems. Some are common in Ubuntu as I could see in the forums, like misbehavior after suspend, other are due to something I did wrong.
Anyway, by trial and error, I got one stable and fast configuration, but trying to go beyond that, I messed something removing packages that I thought were causing the mouse move erratically.
I did a lot of changes, recorded on synaptic history, but synaptic lacks a way to rollback to some point in the past. Or maybe I ignore how to do it.
The other problem is that I installed TeXlive from the DVD, I do not see that LaTeX is installed in synaptic.
My LaTeX system works very well, but I installed other programs in the same way, and I do not know if one of them is causing the problem.
For that experience, I think that synaptic should have a rollback option based on the history recorded by synaptic. BUT it may also be capable to detect other software installed in the system. I suppose that the first change to synaptic is relatively straightforward, I have no idea if the other is possible to achieve, because I do not know if there is a standard directory set where to search the installation status of every program, maybe in /etc maybe in /usr, but I guess that something can be done, because programs not installed form .deb files follow some standard, like
./configure;make;sudo make install which I think is part of autoconf.
Other programs are simply copied to /usr/bin, those are more difficult to find, in part they could be detected by comparing the installed files in synaptic with the directories in the path, that could take too much time, and is not infallible because some strange programs may call libraries or other programs searching in non standard configuration files, certainly those are a very strange case, so strange that it may be the case that such kind of problematic non standard programs are written just for a local installation, by people like me that does not know how to use autoconf or build .deb packages. So those cases should not be a real trouble in practice.
In synthesis: It would be practical to have two functions in Synaptic:
- rollback based on history and
- the search and registration of software not installed via .deb packages.