you can rip as one big wav using eac or use shntool "join" function to achieve the same results. the trouble you're going to have is that the length of the audio will need to be tinkered with a little to get the correct sync with the video (no small feat!).
I've never heard of anybody having trouble like this with audacity. perhaps you could contact somebody on the dev team they like knowing about problems like this and can help out best.
you can also get a trial prog as j. suggests... goldwave is only $50 last time I checked and is really excellent (created by a fine Canadian programmer, I might add).
there's a few other freeware wav editiors but nothing with the same excellent reputation as audacity, so I really hope you get that one working.
here's a link to a few other freeware wav editors I found by googling "freeware wav editor" (minus the quotes)
http://www.nonags.com/nonags/auedit.html
hope this helps
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