Recording Track Output

You can put your amp sim in "input fx". I think that will get recorded to the track when you record. You will have to have another track to record the raw guitar input though.

If you right click the rec button there is an option to record the output which will record the output with amp sim applied

If you were recording the input to a track, you would have an exact copy of what's coming in. Running that through the same fx chain should get the same result... so something must have been different in that trial. If you put an amp sim on a track in Reaper and record the output from that track, you will record exactly what you heard coming out of the sim. I'm going to assume a little too much to try to tie the clues together... Are you recording the direct signal from your UA interface and then using an amp sim in the UA as monitor fx? You will need to see if it has the routing ability and output channels to send the post fx signal back to the computer to record along with the pre fx DI. Worst case if it doesn't would mean you might have to split from the headphone output and record that to another track.