Could it be that you need to fix a bit longer, 1% PFA for 1 hour is
not overkill.  Your times sound good with these tiny little things, but
maybe the time is still too long per change- overprocessing - instead of
the fixation problem.    

If these arteries are as small as human renal biopsies, I do (by hand,
with vacuum) 10 - 15 minutes per change, 20 minutes in my xylene sub,
and two changes of paraffin 30 min each. ( 70, 95 x 2, 100 X 2, and Clearite
3 X 2, followed by paraffin)  All dehydration/clearing is done at room temp.
The automated processing is so efficient, you may be able to shorten times
even more.  I use your schedule to do mouse spleen, gut with peyer's 
patches, and these are huge compared to your arteries.

A good soak after trimming, on ice water may also help during sectioning.

Good luck,

Gayle Callis