I'm experiencing the same issue with a Blackhawk USB560 v2 System Trace talking to an XAM3359 ES1.0 PG1
After power cycle debugger initialization works as expected. In CCS, disconnecting (recompiling or not) and reconnecting the debugger results in a "(Error -1203 @ 0x3D5B) Unable to access the DAP. Reset the device, and retry the operation. If error persists, confirm configuration, power-cycle the board, and/or try more reliable JTAG settings (e.g. lower TCLK). (Emulation package 5.1.340.0)" error.
Choosing "System Reset" from the resets dropdown prior to disconnecting (in an attempt to reach the good state without a power cycle) does not resolve the issue, even though the SoC does exhibit a reset signature. Selecting "Reset Emulator" does not appear to help either.
The previous version of CCS did not exhibit this issue.