The software is different but not too different. If you know how to use one, the other is easy to figure out.
Scid software (Part 2)

Scid 4.6.2 is the most recent version:
https://sourceforge.net/projects/scid/files/Scid/
I'm guessing the Stockfish in your version was Stockfish 2.3 (something) JA. The JA designation means that Jim Ablett did the compiling. Jim is a guru at making fast compiles.
I just played around with both and they are both great! As far as engines are concerned I've downloaded Komodo, Houdini and Deep Rybka (recent versions) and I also have Stockfish 7. So I installed all four engines in both versions of Scid. Those are top 3 engines... Scid has a nice button "Annotate" : you can annotate as many games as you want by using batch setting. And of course, engine does all the work and appends values and
variations/comments. Awesome!!!
I've just downloaded Scid version of the same software (not Scid vs PC). It's version 4.4 and it looks and feels different. Also windows are tiled on the screen and there is only one preinstalled engine - Stockfish and a weird version of it (something like 2.3.... AJ?) I guess that's why it's Scid and not Scid vs PC. Now I have Scid vs PC 4.16 and Scid 4.4. Anybody heard anything like this?