Thank you all for the excellent information provided.
This looks like a bug that was found and fixed after the original CCSv5.5 release. The problem would intermittently cause hangs in the flash component on some PCs depending on the timing of operations.
A fix for this issue is available in the current CCSv6.0 beta-2 release (build 91). There will also be an update to CCSv5.5 available with this fix within a week. The CCSv5.5 update is targeted at a specific device family and is not planned to be made widely available via "check for updates". I will post the link to the update here after it is released.
Unfortunately there is no workaround. Your options are to try the v6 beta, or apply the v5.5 update posted here when it is released.