i have the exact same problem, and more
Time Machine backs up the folder i exclude (TM > Option > + Exclude) every time i run it. In addition, TM fails to back up newly added files contained in folders that are not excluded (most notably newly added mp3s in the Music folder). Btw, i excluded the Download folder, which takes up about 10Gb of space.
Am i doing it wrong? I use a portable HDD (Seagate FreeAgent Go), and i don't keep it plugged in all the time. The only time i do is when i want to do a back up, usually after adding a lot of new stuff into my MBP. After initiating TM, no back up fail message appears, but the stuff the needs to be backed up ISN'T, while those that needn't be IS. I have scoured Google for a solution but so far has found none. I have brought up this problem before here at MR, but no help too. I have tried restarting and even resetting the TM to no avail. Any help from 'experts' would be appreciated.
MBP 09 250GB 2.53
Seagate FreeAgent Go 320Gb
SL 10.6.2 up to date