The best solution to your issue is to use an encryption tool that has a file-model rather than volume (drive) model -- i.e., a tool that provides encryption control for individual files rather than for a disk or partition as an entity (i.e., "full disk encryption").  The advantages to encrypting and managing individual files rather than an encrypted  disk/partition are significant.  Use the former.  Avoid the latter.  You will sidestep unanticipated complications with PC applications, while at the same time maintaining the confidentiality of your files.

An excellent tool for this purpose is SecretAgent by Information Security Corporation (see http://www.infoseccorp.com/products/secretagent/contents.htm). ; It has a solid integration with the Microsoft Office products, and provides for an "AutoEncrypt" feature in which any plain text files (in folders that you choose) are automatically encrypted upon logout.

While the free Windows encryption capabilities or PGP can in principle accomplish the same objective, in practice these tools are simply too cumbersome (in my experience).

Link?