My 05 250 rubbed the tyre on the silencer from new. I discovered after a few rides that the inner muffler was also rubbing on the carburetor. I hated that. I was convinced that the tab on the silencer was welded on crooked and was throwing the rest of the exhaust system out of line, but after comparison with a few other 05 bikes I wasn't so sure. It was suggested that I space it with a rubber washer - I had to use an 8mm thick one to clear the tyre. I didn't like it because it only pushed the inner muffler harder up against the carburettor.
Betas are very well designed, and after discovering that the exhaust parts are machine welded in a jig I changed my thinking - it must just have been the way they were assembled.
Anyway, long story short... The crux of it was the little bracket that attaches the exhaust to the frame near on the left side (which, I think, is only on later models - I'm pretty sure it is not on the 02). I turned it over and clearanced the slots a little. This allowed me to move the inner muffler backwards about 3mm, to the left about 4mm and down about 2mm. It now sits very close to the crankcase (0.5mm), but clears the carburettor. This meant that the bottom end of the silencer mover inwards and the top (noisy end) outwards. I also tweaked the subframe outward a little where the silencer attaches so it lined up neatly with the silencer tag.
This messing about pushed the silencer out and amazingly it clears the tyre perfectly, mud or no mud. No packing needed.
Doesn't help if you don't have the little bracket though?
Cheers
Rob W