There are many possible reasons for this.
Many of them cannot be explained.
Here is one example which is different then your.
A few weeks ago someone had this problem and i was asked to help to solve it.
The problem was ND was installed on three scripts directory.
Apparently some other software was installed in this machine and there are 3 srcipts
directories.
The one the studio uses is not \scripts and some other directory.
Something happened and this directory failed.
Not only you see that can't connect to app server error message but it crashes iis
eventually.
Regenerate nd and only use \scripts directory solved the problem for this one
situation.
One thing I learn from this situation is check iis to make sure it is still ruuning.
User modules that crash ND most likely have java code problem.
It could be linking in some custom packages which cause problem.
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