Scott,
Can you do a complete rebuild and attach a text file with the output of the project you are building (the one where you see two cryptic warnings)? I wonder if something was missing and a .out was not generated.
Also, can you try to manually connect to the board and see if you are able to access memory, registers, etc? For details on that, check the short clip below:
(Please visit the site to view this video)
Also, how is CCS configured? According to this page, the debugger built into the development kit is an isolated version of the XDS100v2, which can reduce the overall debug speed. In this case you could always try to reduce the JTAG TCLK speed on the target configuration file you are using and see if the connection is more stable (for details check this post).
One last remark: CCSv5.2 is rather old and several bugs were fixed in the latest releases, especially in the emulation device drivers (which directly affects the debugging experience). If the target configuration file I mentioned above is ok, I would download and install an updated CCSv5 release (which has updates to the emulator device drivers, the debugger, etc.) and see if you are able to properly debug on the board.
If you install this new release in a different directory and use a different workspace you will not have any problems in damaging your existing CCSv5.2 install.
Hope this helps,
Rafael