If you are using a very old version of VB.net, it's possible, but not likely, that you may be running out of cookie name space as it was a lot more limited than modern web servers.
If you still have problems, please contact support and they'll be able to talk you through it, and help you troubleshoot.
We're a .NET stack as well (but C#) and pleased to say we have absolutely no issues with TiQ (including working with the datalayer).
I would suggest trying everything without deviation - if you can keep to the common standard then all the better (and as @steve_lake mentioned, you likely won't have any issues). With so much great reference material here, it really helps being able to directly apply examples without having to do a bunch of special adjustments to make it work with a non-standard setup.
Your JS should run just fine in any APSX file.