You may want to post this on the triathlon board- you might get more responses there. It could be a number of issues. I don't have problems doing tris in my tri shorts (and I run in them all the time on normal training runs anyway) so I'm not sure what the issue is, but I have some suggestions that may work. I would suggest trying the chamois butter then doing a test run of the tri. Swim for a bit, then get out and cycle then run for a bit (can be really short- maybe 5 min swim/15 min bike/10 min run just to test it out). Don't know if chamois butter is "waterproof" or not. You can also try bodyglide- that IS waterproof. There's also this new stuff out there called Aquaphor (from the makers of Eucerin- I think you can find it at drugstores- it's a skin protectant that is basically like Bodyglide, but is in gel form that you can apply on the spot) that works really well. Try using some of that to test it out. It may be just a matter of trying some different things to see what will work for you. Perhaps it's just a matter of getting your bits used to running with the tri shorts.
Whatever the reason, I hope you find a solution that works for you. I wouldn't worry about taking more time off, I think you should be fine if you want to start running again.