I wonder what role that agreement plays into this suit.
If they're making money licensing patents to competitors, then it doesn't really matter if they have a competing product coming out. They either make money or make money... its just where it comes from that changes.
Only after about a year of negotiation over cross licensing failed to reach an agreement did both sides file suit. Yes, Microsoft got their suit filed first, by about a month or so. However, it takes several months to prepare to file a patent suit, so it's clear both sides had been working on it for a while.
As far as I've been able to find, there's no public information as to who actually was the initial aggressor between Microsoft and TomTom. But given that up to that time Microsoft had not sued anyone over software patents, and has not sued anyone since then over software patents, and that TomTom had sued people over software patents (in Eastern District of Texas, even), it seems likely that TomTom was the aggressor.
HTC said when this first showed up that Apple's lawsuit caught them off guard, so it naturally took a bit of time to figure out what patents Apple was infringing on.