I am also having this problem on T4_blank. Modules sometimes show up, other times they don't. It seems to only affect some module positions, but because its intermittent, I don't say that with great confidence.
I have caching completely disabled, but T4 is still creating files in the /cache/t4/ directory, and clearing the cache seems to temporarily correct the problem, so it seems like it has something to do with the T4 caching.