I have been caught out by this in the past myself and a colleague wasted a great deal of time trying all sorts of things only to find out there was a simple fix to all his connectivity woes.
Since the introduction of the 64-bit operating system we have seen applications become split into 32-bit (x86) and 64-bit (x64) branches. While the introduction of 64-bit was a god send for the application developer and server administrators who had been looking for ways to push more memory to applications to allow them to handle the huge tasks that today's business (and sometimes even the home user) wants to throw at them. The unfortunate down side to this was that 32-bit applications were cast out like the lepers of the Bible days and given their own registry space (ahhh you say, now he gets to the point of this, well all I can say is that it was worth it!!!)
If you don't know 32-bit and 64-bit applications have different registry spaces, because 32-bit applications cannot read anything within 64-bit memory. If you were to look at the registry on a 64-bit operating system it may not look different to the naked eye but if you look closely you will find that there is a new branch HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node and it is here were all the 32-bit applications store their registry settings.
So why is this important to anyone that has anything to do with database connections, because as you would be aware SQL Server allows you to configure Client Alias's within it's Configuration (of the connectivity tools) and it is through the use of these Alias's that we can map a Server Name (or even a made up friendly name) to a FQDN server address and non-standard TCP port. The problem is that on a 64-bit operating system there are both 32-bit and 64-bit Client Alias and depending on what the application you are connecting from is will depend on which type of alias it tries to read.
The times that I have usually come across this as a problem is when an installation package is asking for the SQL Server details of where it will create a database and the user is unaware if they are using a 32-bit or 64-bit application and create the Client Alias in the wrong branch.
So my rule is:
When you setup a Client Alias always set it up in both the 32-bit and 64-bit branches of the SQL Server Configuration Manager.