Never had problems with long files. In fact libpcap is who manages the file so it shouldn't be any problem.
For weplab the point is not how large the file is, but how many encrypted data packets does it have. I have never tryied to run weplab -r with more than 3M packets (mainly because it is not neccesary so many packets to break the key).
Please, issue the 3 commands I gave you in my last post (using --debugkey with your real key), and post the results.
Dont forget to use the option --key 128 if your key is 128 bits long.
PD: new version of the README at
http://weplab.sourceforge.net/files/README