The only thing I know about generating the code and the Source Safe, is that LLBLGen always re-generate the classes and if nothing is changed, they will be detected as changed by Source Safe, because LLBLGen writes a Timestamp in all the generated files, that's why they might appear as different versions.
To overcome this issue , just set TdlEmitTimeDateInOutputFiles in the project properties to false. This is an inherited property from the preferences, so for future project, also set it in the preferences.
And then no timestamp will be emitted in the generated files.