The events generated in those threads will be specific to those threads, thus your main loop will not see them (this makes sense if you think about it, each thread could theoretically be running it's own UI, and if the events from those threads were seen by the main thread all kinds of not-so-fun things would end up happening). Luckily, CVI has a very nice mechanism for passing messages between threads, they are called Thread Safe Queues. You can enqueue items in one of these from your threads, and install a queue callback using CmtInstallTSQCallback with your main thread which will be called whenever items are placed in the queue.
Best of luck,
Ryan K.