I looked around for another thread about this...

I bought a NES the other day and everything is working fine with the exception of a few sprites. For example, when I start up SMB3, everything works except that Mario and the enemies are invisible. I can still play the game as if Mario were there, hit the question mark boxes, die, etc. It's not the game because it works on my other NES. Anyone have a clue about what's wrong? Should I just clean the contacts, or is the problem more serious?

Sounds like 1 of the wires that goes from the GPU is broken. I've had the exact same problem, but on a cart instead. 1 wire was cut off and several of layers of the gfx was missing. Game started without a problem, but it was unplayable due to the missing gfx, didnt see anything what was going on hehe.

If it does the same thing with different carts too (invisible sprites, rather than garbage sprites) that is very odd indeed.

Doesn't sound like a contact problem (try other carts to see).  I doubt it's a defective PPU.  And it's very unlikely the trace on the mainboard is broken (unless it's corroded or something).

I have tried other carts and similar things occur. For instance, on the loading and title screen of Snake Rattle and Roll everything appears but the twinkling stars in the background and the little doodad that moves to select one player or two players. So, it seems it has something to do with graphics that move. I'm gonna check the wiring soon to see if anything is disconnected.

Have the pins been "fixed" - bent so that they work better? They can snap even on the first time since these units are getting so old collectively. This would be more likely than anything happening to the PCB. Getting a replacement pinset is never a bad move anyways.