Good point rsefton. I forgot about that, and if the signals are missing just because they're not post-fit(but they do exist in the design), then my previous message can be ignored.
Post-Fitting is most useful if you set your Top partition to post-fit. You can now keep the design locked down and do quick SignalTap compiles(as SignalTap is another partition that is therefore synthesized independently, and with Top locked down, placed independently). So it's a nice way to do quick SignalTap compiles and to debug anything that might change compile to compile. But you're also stuck looking at post-fit nodes.
If you go to pre-synthesis, you have a lot more options and they make sense, but you must run a complete compile from scratch to get it to work. Often users don't care, but those are the trade-offs.