|Just another Perl shrine|
The idea of filing a notice of prior art and then having the PTO reject your notice as "not prior art", sounds very interesting to me and definitely worth discussing with a patent lawyer. Better to have that determination made early on by the PTO than after the fact in a court of law.
Contacting IBM (with the agreement of your lawyer) may not be such a bad idea either. Patents are normally written in as broad a language as possible and only narrowed when the PTO or others claim prior art. All this costs money and IBM may actually be grateful for a heads up that their patent language is overly broad. On the other hand, they may also disagree with you - in which case you can follow tanktalus's advice and keep the communication documented. If they do later on try to claim infringement, you can use that communication to show that at one point in time IBM itself admitted that there was no infringement.
As far as documenting the communication, this also needs to be discussed with your lawyer. Emails are evidence, but not as strong as a letter written on company letter head with a signature of an authorized employee. The latter is much harder to forge.
An ounce of prevention is worth a pound of cure
And in this case it might be a hell of a lot cheaper.
Update: fixed some unclear wording