I am having the same issue.
I created a Speedpak of a 4 part subassembly
This subassembly (speedpak) is then patterned ~150 times within another assembly.
Every time I Ctrl+Q rebuild the assembly, every other speedpak suppresses itself. Not sure how to prevent this from happening.
Wish I could help, but I never found an answer. I had a dead line to finish the job, so I turned off all the speed packs and carried on.