SD Card Initialization Failing with MSP-FET Connected, works without

First off, my setup.

IDE/compiler:  IAR EW430 6.50.1
Programmer: MSP-FET  (Jtag speed set to Medium in IAR, also have tried with Fast)
Micro: MSP430FR5969
SD Card:  Kingston microSD 16GB SDHC as well as 64GB and 1GB cards

I am trying to integrate Chan's FatFS on the MSP430FR5969 designed into a custom PCB.  I am able to initialize the SD card (put it into Idle State, then put it into run mode).  The issue I am having is when I have the MSP-FET connected, I have three problems:

1.   It takes about 1.3 seconds for the SD card to go into run mode (it should take hundreds of milliseconds)
2.  The data received from the SD Card indicates a SDSC, when the card is actually an SDHC
3. Once initialized, the SD Card returns an invalid command to a read block request

I post this here because when I remove the MSP-FET, the SD card:

1. Initializes in 0.14 seconds
2. Reports back as SDHC
3. Allows Block Request commands

I'm wondering if this has to do with clocking from the MSP-FET, or some setting that I can change (hopefully).  It's going to be difficult to debug from here out if I have to disconnect my debug tool every time.

Thanks for the help in advance!
-MC