I have lots of pirate famicom carts (including many of those crap yellow ones), and I haven't noticed anything like that. I know some of them work better on famiclones than real hardware, but I haven't seen any difference between nes and famicom. I only have an AV famicom, though I've never tried with one of the older ones.
Edit: can you confirm whether or not other (licensed) games also have this issue? Maybe it's a problem with your famicom?