Hi Jeroen,
I understand you do need your projects to be on the server so that others in your firm can access them. The reason I asked to copy the troubled files locally it was to test and see if the issue will persist locally to rule out the possibility of others making those changes without your knowledge, if it is an intermittent issue then perhaps might be file related but if the issue started right around the time when "compress on exit" was set then yes see if by disabling this option makes any difference on the troubled files.
I understand you do need your projects to be on the server so that others in your firm can access them. The reason I asked to copy the troubled files locally it was to test and see if the issue will persist locally to rule out the possibility of others making those changes without your knowledge, if it is an intermittent issue then perhaps might be file related but if the issue started right around the time when "compress on exit" was set then yes see if by disabling this option makes any difference on the troubled files.