Hi Drandre,
you are right, this problem makes no sense and I'm sorry to hear that you lost your logs. It could have been a bug in Messenger Plus! causing it not to notice this specific chat you had... I know it soudns strange but I recently fixed a problem like that and the fix will be part of Messenger Plus! 3.60, due in September.
When this version will be out, I encourage you to download it and email me at mplus@patchou.com if you notice anything else of this kind again. I do not want this kind of problem to be in my software more than you
.