diff --git a/HSBencher/App.hs b/HSBencher/App.hs
--- a/HSBencher/App.hs
+++ b/HSBencher/App.hs
@@ -342,7 +342,7 @@
   let (diroffset,testRoot) = splitFileName testPath
       flags = toCompileFlags cconf
       paths = toCmdPaths     cconf
-      bldid = makeBuildID flags
+      bldid = makeBuildID testPath flags
   log  "\n--------------------------------------------------------------------------------"
   log$ "  Compiling Config "++show iterNum++" of "++show totalIters++
        ": "++testRoot++" (args \""++unwords cmdargs++"\") confID "++ show bldid
@@ -860,7 +860,7 @@
                 -- a directory that is used for `RunInPlace` builds.
                 let (bench,params) = nextrun
                     ccflags = toCompileFlags params
-                    bid = makeBuildID ccflags
+                    bid = makeBuildID (target bench) ccflags
                 case M.lookup bid board of 
                   Nothing -> error$ "HSBencher: Internal error: Cannot find entry in map for build ID: "++show bid
                   Just (ccnum, Nothing) -> do 
@@ -882,7 +882,8 @@
                         -- Here we know that some previous compile with the same BuildID inserted this here.
                         -- But the relevant question is whether some other config has stomped on it in the meantime.
                         case M.lookup (target bench) lastConfigured of 
-                          Nothing -> error$"HSBencher: Internal error, RunInPlace in the board but not lastConfigured!: "++(target bench)
+                          Nothing -> error$"HSBencher: Internal error, RunInPlace in the board but not lastConfigured!: "
+                                       ++(target bench)++ " build id "++show bid
                           Just bid2 ->
                            if bid == bid2 
                            then do logT$ "Skipping rebuild of in-place benchmark: "++bid
@@ -891,7 +892,7 @@
 
               initBoard _ [] acc = acc 
               initBoard !iter ((bench,params):rest) acc = 
-                let bid = makeBuildID $ toCompileFlags params 
+                let bid = makeBuildID (target bench) $ toCompileFlags params 
                     base = fetchBaseName (target bench)
                     dfltdest = globalBinDir </> base ++"_"++bid in
                 case M.lookup bid acc of
diff --git a/HSBencher/Types.hs b/HSBencher/Types.hs
--- a/HSBencher/Types.hs
+++ b/HSBencher/Types.hs
@@ -264,14 +264,16 @@
 type BuildID = String
 
 -- | Performs a simple reformatting (stripping disallowed characters) to create a
--- build ID corresponding to a set of compile flags.
-makeBuildID :: CompileFlags -> BuildID
-makeBuildID strs =
-  intercalate "_" $
-  map (filter charAllowed) strs
+-- build ID corresponding to a set of compile flags.  To make it unique we also
+-- append the target path.
+makeBuildID :: FilePath -> CompileFlags -> BuildID
+makeBuildID target strs =
+  encodedTarget ++ 
+  (intercalate "_" $
+   map (filter charAllowed) strs)
  where
   charAllowed = isAlphaNum
-
+  encodedTarget = map (\ c -> if charAllowed c then c else '_') target
 
 -- | Strip all runtime options, leaving only compile-time options.  This is useful
 --   for figuring out how many separate compiles need to happen.
diff --git a/hsbencher.cabal b/hsbencher.cabal
--- a/hsbencher.cabal
+++ b/hsbencher.cabal
@@ -1,6 +1,6 @@
 
 name:                hsbencher
-version:             1.1
+version:             1.1.0.1
 -- CHANGELOG:
 -- 1.0 : Initial release, new flexible benchmark format.