I use the following configuration for my latex projects, all under version control:
trunk/
tmp/
out/
bib/ # In fact a symlink
project.tex
chap1.tex
other.tex
When I use TexLipse Center WITHOUT a svn client configured in Eclipse, it copies the full content of the tmp folder to the main folder after a compile, including the ".svn" folder of the tmp dir. This corrupts the current checkout, since the ".svn" folder of trunk/ is overwritten. The only way to stop this behaviour is to install a svn client in Eclipse (I tested only with Subclipse).
I think the fix is not complicated and I started to look on it.
By the way, thanks for the great Latex editor! :-)