Well, if having problems due to fragmentation of the memory almost *anything* can trigger the problem. That's why such issues are often found late, because you add a scmall feature thinking it's save, but afterwards the problems may start...
So the normal queues may lead to a small fragmentation. Maybe you won't notice this for a long time without any other code interfering (the code needn't to be related neccessarily!), because it's just a small fragmentation. But as the file writing seems to handle quite a amount of data (array? strings?), the fragmentation starts to get serious and you'll experience problems quickly. Maybe even the file writing routine (or things you're doing around) aren't RT save and lead to fragmentation too.
One problem I always have in LV RT is, that following the NI documentation, a string is an array of char, or better something like *char, that means a *dynamical* array of chars. If that's true, even an extensive use of strings and string operations may lead to problems! Unfortunately you can't define fixed chars in LV...
Regards,
Carsten
(There's a reasen, that NI recommends just using RT queues in a RT environment...)