SignalTap Can't Read Certain Signal

It sounds like perhaps you've been tapping post-fit signals instead of pre-synthesis nodes. The weird names in the image you attached seem to confirm this. If changes are made to a design, there's no guarantee that post-fit signals will remain after another compilation, so Signaltap can't connect to them. I rarely tap post-fit nodes because of this. If you can, tap pre-synthesis nodes. These are also much easier to find because they are based directly off your HDL design. Use the Node Finder in Signaltap set to the pre-synthesis node filter or cross-probe to Signaltap from the RTL Viewer, not the Tech Map Viewer.