Hi Aaron,
1) Please uninstall MQE from add/remove programs (Make sure that you also uninstall the bindview support services as well).
2) Go to BV-Config and go to edit ECS database and please delete the entry of MQE and Support service from there and save.
3) Manually run the MQE setup, during the installation GUI please uncheck the default settings box so that you will be able to get the option to specify the "E" drive.
4) Once the MQE is installed, make sure that you have downloaded the latest hotfix and apply both to RMS as well as one new MQE.
5) Once the hotfix is applied on RMS. It will dowload the lastest hotfix for MQE in QE hotfix folder. It should be located in RMS\windows\control\QEhotfixes. select the latest one sort from date.
Please let me know how it works