did you buy the Janome from a nearby dealer? if so, take it there so they can give it a look-see.
does it knot and clump at the beginning of your seams. you shouldn't need to, but try holding onto the tails of the top and bottom threads as you begin your seam. pull them out to the back, fairly taught as you sew the first few stitches.
for just plain sewing, my janome is happy enough with just about every thread i've tried, so i wonder what would happen if you tried a different brand, type and/or size needle. while i'm sure there are other brands just as good, mine is quite happy with schmetz needles. definitely happier than it was with the singer needles i bought at walmart. (not criticizing either singer or walmart, here. the schmetz just happen to work better in my janome - especially when i want to use the automatic needle threader thingie. the singers just don't line up right. i usually had to give up on the thingie and thread them the hard way.)
different needle types have differently shaped eyes. according to everything i've read online, that can make a big difference in how well they get along with different threads.
just a thought. or two or three.