I myself have not encoutered this problem, but I haven't played through the main campaign in a while, and not with a recent build. At present, FS2 has been rather sluggish on my system, so until I upgrade my specs, I'll be restricting my Freespacing... but I digress.
I have however, encountered an odd problem of FS2 apparently ignoring IFF. Every time I play the mission from the Port v2.3 when you're supposed to capture the HOL cruiser Ramses, but the Taranis crashes the party, the Shivans don't fire on the Ramses like their supposed to. They shoot at pretty much anything else, but not the Ramses. Maybe this is another symptom of the same problem... FS2 deciding to change IFF of a ship without being prompted to do so by scripting. The Ramses becomes (or is seen by 'Hostile' ships as) Hostile rather than 'Neutral', and a similar IFF change is taking place in your situation. Either Lambda 2 is becoming hostile/neutral, or the Massana is. Take another look at the mission and see if there is a change in IFF of either ship.