The version of FTMM you're using is not supported vis-a-vis Yosemite. This means the software is not being tweaked (patches, etc) to keep up with computer OS. It's baffling (well, not really, ACOM is hopelessly Mac unfriendly) ACOM customer service didn't tell you that.
You're likely to encounter more issues as time goes by. I suggest you call ACOM and express you want to upgrade to the newest version and would like the best deal possible, (my last upgrade was $20). The new version is the more stable than all previous versions and optimized for Yosemite.