My setup - I have a F28035 in a Dock Kit connected via a JTag V100. I also have a Innomaker USB to CAN attached to GPIO30 and 31. I also have a Logic 2 CAN bus analyzer attached to these GPIO pins. The CAN design is such that it never transmits any message unless requested. I have a Visual Studio program that I use to send the CAN messages to the F28035 and all F28035 responses are as expected. (One of the CAN requests is a BIT message which will be stuffed with any faults found.)
When I load my program into flash via Code Composer/JTag and start the program, the CAN bus behaves as expected - no transmission of data unless requested. I have set breakpoints at the ISR and the CAN_SendCmdMsg() of which neither are hit when the flash program is started. Also, the Logic 2 analyzer on the CAN bus shows no activity upon program execution.
When I power cycle the F28035 so that the program in flash will be executed, the F28035 CAN transmission line is being hammered with garbage words - with or without the Innomaker attached to the GPIO lines. (The BIT message is revealing that EPIF0, WDIF0 and MTOF0 flags are set.) I have another ticket open to see how to connect to the running flash in Code Composer but I was wondering if this sounds familiar.
If I get more data, I will update this ticket.