I would probablly say its your capfile. I would try striping it with tshark or with the pyrit strip option. As you can see using aircrack's test file it works fine.
root@bt:/pentest/wireless/aircrack-ng/test# /pentest/passwords/crunch/crunch 8 8 abcdefgh | pyrit -e test -i - -r wpa.cap attack_passthrough
Pyrit 0.3.1-dev (svn r228) (C) 2008-2010 Lukas Lueg pyrit - Project Hosting on Google Code
This code is distributed under the GNU General Public License v3+
Parsing file 'wpa.cap' (1/1)...
13 packets (13 802.11-packets), 1 APs
Picked AccessPoint 00:0d:93:eb:b0:8c automatically...
Tried 3140157 PMKs so far; 8068 PMKs per second.