Finally figured it out, after trying all sorts of things including installing different versions of scid vs. pc on multiple OSs and trying different .pgn files and different databases, both new and old. The .pgn file I was using only contains positions, not complete games. On newer versions of scid vs. pc, the batch annotate does not work for PGN files containing only positions.
SCID vs PC

I've never tried that but I would think you can get it to at least evaluate the position and insert a score. Based on the way the auto-annotate feature is designed, I don't see that it would do more than that.
Did that work before?

Hi guys, I have a question please.
How do you change the disturbing green color of the annotation text? It's horrible and it hurts the eyes very bad.
Thanks!

Hi guys, I have a question please.
How do you change the disturbing green color of the annotation text? It's horrible and it hurts the eyes very bad.
Thanks!
Assuming you are using windoze:
Find the file options.dat (it's in the C:/Scid vs PC_version/bin/config folder).
Open with a texteditor (even notepad would do).
Find the string set pgnColor(Comment)
Replace the color value (HEX values of colors can be found on thousands of internet sites). Save, exit, and restart the program.

Yes, it worked both ways. Thanks a lot!
The interface is a bit stupid, I have a lot of space on the screen but the board is still small. I think that's because of the text above the table. Is there a way to remove it so the table can be larger?

I don't have this.This space is used to show material differences/gains.
Is "auto resize board" (under Options/ Windows) checked?

@TawMoto I use scid vs. Mac and I can just drag the line to left and right easily, just by grabing the line and moving with the mouse

I checked and unchecked the auto-resize and the result is the same...I will get used to it. Thanks.
Only one questions and I am gone.
Is there a possibility to change the default number of lines of the engine? Because it's always 1 when I restart SCID.
Also, the font size of the engine lines would be nice to change, too...

how to set the new peices to Scid vs pc ?
I haven't done it myself, but the instructions are on this page, thanks to Ed Collins:
http://www.edcollins.com/chess/scidvspc/helpful-tips.htm

A file with multiple FEN positions should be formatted just like any other PGN file. The only difference is that no moves are listed for each game.
i was watching a game of chess in scid. at a certain point, i think an alternative move. i made the move for white . then i want to see what is the reply of the engine to it. how can i accomplish this task? I dont want to get the analysis of the move but a reply for the move just made by me.if i made the move for white the machine should make a reply move from black's perspective.

You need to just have the analysis running in the background. It won't make the reply but you can see the suggested lines.
i was watching a game of chess in scid. at a certain point, i think an alternative move. i made the move for white . then i want to see what is the reply of the engine to it. how can i accomplish this task? I dont want to get the analysis of the move but a reply for the move just made by me.if i made the move for white the machine should make a reply move from black's perspective.
go to "play" menu, select either 1 " serious game" or 2 " tactical game" from the drop down menu; later select " start from current position"...
you can see what engine will reply with and you can play against it
Hello, I have a question about SCID vs PC. Is it possible to use the interface to connect to fics as guest and have a chess engine play online?

Hi everyone.
I use Scid vs. Mac. My question is regarding databases. I created a database of all my games. I'd like to know whethere there is a way to find the games with some specific pawn or piece set-ups in the database. For example, can I find all my games with white pawns on e4-d5-c4 vs. black pawns on e5-d6-c5? I guess there is the option in Chessbase, so I hope there is something similar in Scid vs. something!
OK, had a chance to try this. Created a new database. Added some games. Started the engine, clicked the auto-annotate feature, changed the setting to batch annotate, and it worked as expected.