Are there any common problems with the top loading NES / clone systems? Nothing's wrong with mine - just so that I know for future reference. For example - obviously the games are designed to be front loading, but are not etc. and does this cause any glitches down the line? That sort of thing, or any problems comparative to the 'blinking' light on the original NES etc.

Well your never going to have a blinking light in anything but a toaster.  The blinking light syndrome is caused by the copy protection chip and that's only in the toaster NES.

I have a Yobo famiclone which I use the most.  I like it a lot, which is why I use it more than my toaster, but here are some problems I've noticed.  

1) The sound in some games is off a little, which is a result of flawed sound emulation.  I rarely notice it, but it's very easy to notice in Super Mario Bros., and my SMB2j reproduction.
2) Due to the shape of some unlicensed cartridges, they actually don't fit into the cartridge slot.
3) The Yobo has great compatibility, but for some reason I can't friggin play Mega Man 6.  I tested 2 different carts, and they both don't work.  Yet it plays CV3 flawlessly.  Go figure.

That's all good info. cheers! Just means I know what to watch out for in the future!  :)