First, Welcome to the forums!!!!
Second, now that we got the pleasantries out of the way lets dive in. Do you use the stock phone app? What version is your device on? and Have you rooted or installed a custom rom on it?
The two things I can think that may be happening is the third party messages app is not playing nicely with your phone and the stock messaging app. When you have third party app - your messages are still getting registered in the stock app as far as I know and if the two are not playing nicely there could be a cause for the app to crash and delete your info.
The next thought is if there is something in your system that is crashing and losing the info. Call log should not be effected if you are using stock app and I do not think there is a limit of how much log you can keep. The only time I have personally found that part to be deleted is if my system crashes (coz I am an individual that touches things and definitely not the correct ones) or if I flash a rom. I like to backup these things every so often - mybackupro is good one for backing up call logs and texts so you have them.
Anyway I would suggest doing a few tests of apps and scenarios and seeing if you can replicate the problem. If there is a specific set of things that you can identify after which your stuff is deleted it narrows the plain field.
Hope this helps!