This thread is a few months old now - since it was posted we made some fixes our end which seems to have helped, and I'm pretty sure it only affects a small number of users, since lots of people use it on Steam but we don't get many reports of these types of issue. If there's still trouble though then it sounds likely it's Steam that's causing them. The Steam version of Construct 2 is almost totally identical to the one we publish on our site. The biggest difference is just that it checks with Steam if it's been purchased or not as opposed to using our own licensing system, which is a relatively small and simple change and it's hard to imagine that causing a variety of weird issues like you describe. On top of that everyone always reports the version from our site works OK (which is weird since it's almost identical) and
SecondDimension's report seems to correlate problems with Steam activity, which seems to be further evidence towards Steam causing the problems.
I'll follow up again with Valve and see if anything can be done. If you really have trouble then I'm afraid the best course in the short term would be to get a refund from Valve (we can't do this for you - Valve handle all payments and accounts on Steam) and purchase again directly from us.