BizTalk 2013 CU2 + ESB : Failed to update resources in the application - biztalk

Question

Recently upgraded to BizTalk 2013 CU2 and installed ESB.
This has had some side effects as we can no longer deploy without getting a database FK reference error.
Any one seen this before?
Here is the error when we try to deploy a new assembly to the DEV environment.
TITLE: BizTalk Server Administration
Failed to update resources in the application.
ADDITIONAL INFORMATION:
Failed to add resource(s). (mscorlib)
Change requests failed for some resources. (Microsoft.BizTalk.ApplicationDeployment.Engine)
BizTalkAssemblyResourceManager failed to complete end type change request. (Microsoft.BizTalk.ResourceManagers)
Removal of the assembly failed. Make sure that all items in the assembly you are trying to remove fulfill the following conditions:
Pipelines, maps, and schemas are not being used by Send Ports or Receive Locations in the same or referenced application(s).
Roles have no enlisted parties.
Database Error:
The DELETE statement conflicted with the REFERENCE constraint
bts_receiveport_transform_foreign_transformid. The conflict occurred
in database "BizTalkMgmtDb", table "dbo.bts_receiveport_transform",
column 'uidTransformGUID'. The DELETE statement conflicted with the
REFERENCE constraint "fk_bt_mapspec_bts_item". The conflict occurred
in database "BizTalkMgmtDb", table "dbo.bt_MapSpec", column 'itemid'.
The DELETE statement conflicted with the REFERENCE constraint
"bts_receiveport_transform_foreign_transformid". The conflict occurred
in database "BizTalkMgmtDb", table "dbo.bts_receiveport_transform",
column 'uidTransformGUID'. The statement has been terminated. The
statement has been terminated. The statement has been terminated.
(mscorlib)
I ran a SQL trace and found that this is the SP that breaks when it tries to delete from table dbo.bt_MapSpec.
exec dpl_DeleteAssembly
#Guid=N'00000000-0000-0000-0000-000000000000',#Name=N'theassemblynamegoeshere',#VersionMajor=1,#VersionMinor=0,#VersionBuild=0,#VersionRevision=0,#PublicKeyToken=N'89e32fae0caf808e',#Culture=N'neutral',#Type=N'2',#NoSchemasVerify=0