Thanks for the log Mark, I will take a look at it shortly.
The user guide says it's best to leave PF3 to handle the climb profile, that's why PF3 puts your cruise altitude into the first waypoint and handles it from there. The descent profile however is a different matter and it's always best to see what PF3's profile is like and make any adjustments you feel necessary.
Incidentally, I was able to recreate the pause issue you were having once I'd updated to the most recent FSUIPC. It appears there were some changes with the way 'pause' works in MSFS and therefore some changes made in FSUIPC. I've now got that working correctly and it will be in the next beta.
I have not, however, been able to recreate your sim rate issue and was wondering if you still had that problem (I will know of course once I check your log)
Thanks again I'll get back to you with my findings.