I have a boss DD-3 delay and I have noticed that when I have the delay time up quite high, the repeated signal becomes really fuzzy. I am running it through the effects loop of my Marshall JCM2000 DSL 401. Can anyone shed some light on this?

I dont know what its called on your amp, but I had the same problem on my Traynor and all I had to was adjust the loop return and send pots on my amp. Try playing with those knobs a bit.
ESP/LTD EC1000 (w/ EMG 81 and 60)
ESP/LTD H500 (w/SD Custom 5 and 59)
Fender MIM Strat (basically my first. Never play it.)
Traynor YCV80 4x10
Peavey 6505 2x12 combo

Half Stacks are OVER-Rated
The DSL 401 has a parellel effects loop, meaning the amp tone runs along side of the effects. This may be causing the sound you discussed. The 401 effects loop is really not that great (and I dig the tones from the 401!) you may want to try putting your effects in fron of the amp. Sorry, I don't have a better answer and good luck!