I ran across this issue when building my HIPAA Schemas in Release mode for deployment.

(-1040) The engine input file compilation process is already active

There are good reason for receiving this, such as, someone else doing a compile and/or accessing the EIF file at the same time you are. If you are sure that is not the case then you can manually unlock the repository. Do do this open Query Analyzer and run this script:

USE BizTalkHIPAA_EDIDb
GO
UPDATE parame SET repolock= NULL
GO

What initially caused this issue was, at one time I was building the Schemas and I canceled the build which killed the COMPEIF.exe process leaving the table in a locked status.

Ed K.