Thats wierd....It should work from what you are telling me. Try increasing the fudge factor a little. Technically you shouldnt have to but thats all i can think of. If nothing else turn it way up over night and see what happens...
its the -f <#> function. Default is -f 2 i believe. So this is what it would look like:
aircrack-ng -f 6 file.cap
EDIT: oh, make sure when you are running airodump-ng you have all the setting like --bssid and --channel set to filter out unwanted junk. You might have a bunch of random .ivs which would be hard to crack