Hello
I have the same problem...
In cmd I see this when I creat the db new

ERROR - 1486617937: (..\BlockDataMap.cpp:79) merkle root mismatch!
-ERROR - 1486617937: (..\BlockDataMap.cpp:80)    header has: xxx
-ERROR - 1486617937: (..\DatabaseBuilder.cpp:353) block deser except: invalid merkle root
-INFO  - 1486617937: (..\DatabaseBuilder.cpp:268) parsed block file #278
-DEBUG - 1486617937: (..\Blockchain.cpp:242) Organizing chain
-INFO  - 1486617947: (..\DatabaseBuilder.cpp:56) updated HEADERS db in 682.79s
-INFO  - 1486617947: (..\BlockUtils.cpp:1636) Enabling zero-conf tracking
-ERROR - 1486617947: (..\BlockDataMap.cpp:79) merkle root mismatch!
-ERROR - 1486617947: (..\BlockDataMap.cpp:80)    header has: xxx
-ERROR - 1486617947: (..\BlockDataMap.cpp:81)    block yields:xx
-ERROR - 1486617947: (..\DatabaseBuilder.cpp:353) block deser except: invalid merkle root

how I can fix this...  or better question how I get my BTC :-(
regards