If your sole concern is patent liability, you're probably ok. IBM has given some general assurances that it won't hold patents against open source software. Of course, saying and doing are two different things, so "probably ok" in the court of law may not be exactly comforting. Besides, the patent going through can confuse issues of originality and novelty, which may damage your company's reputation.
If you're really concerned about invalid patents, and this isn't just about protecting your company's bottom line from liability (which there's nothing wrong with, just pointing out that different motivations may have differing approaches), then you may want to try to contact IBM itself. The IBMer in question who filed the patent is listed - you should actually be able to get in contact with him. A quick google for ibmer phone number reveals a way to find IBMer information by going to http://whois.ibm.com and plugging in the name. It's no good for finding a list of IBMers, but if you have a name, and they're still employed by IBM, you can get that person's email address and phone number fairly easily. I'm not sure a phone call is necessarily the best, perhaps an email to start, but at least it's something. I think it goes without saying, but of course you should be professional about it and not harass the guy, just point out the prior art. Further, if you do have any communication with IBM about it, keep notes. After each communication, keep a written log. If it's email, this is easy - just print out the emails, or at least save them in an archive to make the conversation easy to follow. As long as we're dealing with legal issues here (and PTO is about the law, not about technology), you should keep notes. IBM has plenty of lawyers - you're not going to outspend them, so you better make sure you have everything written down so that your lawyer can either get you out before you spend too much or can win a defense on the cheap. Hopefully, of course, it wouldn't get that far (see "general assurances" above), but better safe than sorry, since you seem to already be concerned about it.
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