This is a Known issue in the current release of ISSM (It is mentioned in the release notes).
Please check that there are no running GDB sessions before you start flashing - Intel® Quark™ Microcontroller D2000 - Flashing status indicator only reaches 99%
Let me know if the issue persists after all GDB sessions are closed (you can try restarting Eclipse also).
i check this issue is 32M Hz Clock not work .
we change another 32M clock is good work now .thanks ~