What version is the template you are using?
There used to be an issue with the older version of the appstacks that they had a drive letter assigned in the template, you can edit the template appstack by attaching it to a machine without Appvolumes agent and do the following.
Run diskpart and select the appstack volume then run the following command
attributes volume set nodefaultdriveletter
You can check it it worked by typing in the command attribte volume.
The value for No Default Drive Letter should be Yes.
Also, you could try looking at this registry setting, it will force hide the appstack driveletter for you (does not always seem to work 100% though).