I'll stick my neck out and post this as an answer because it's not formatted nicely as a comment.
Have you tried this:
sp_MSforeachtable "EXEC sp_CompareTable dbName1, dbName2, NULL, PARSENAME('[?]', 1)"
Update:
It looks like it doesn't like the PARSENAME. You could try this (I tried this on a version of sp_CompareTable with the EXEC changed to a PRINT).
Add this line to sp_CompareTable (before the EXEC):
SET @TableName = PARSENAME(@TableName,1)
Call it like this:
sp_MSforeachtable "EXEC sp_CompareTable dbName1, dbName2, dbo, '?'"
NB: This would be a quick fix for the case where you only have the "dbo" schema. It doesn't really answer the question of exactly why the original syntax doesn't work.
Update Again:
Here's a version of the Compare Table stored procedure which is tailored to run with sp_MSforeachtable
CREATE PROC [dbo].[uspCompareTable](@db1 varchar(250), @db2 sysname, @TableName sysname)
AS
declare @reason varchar(7)='Missing';
IF @TableName = '[dbo].[sysdiagrams]'
RETURN
IF CHARINDEX('.',@db1,1) <> 0
SET @db1=QUOTENAME(SUBSTRING(@db1,1, CHARINDEX('.',@db1,1)-1))+'.'+QUOTENAME(SUBSTRING(@db1, CHARINDEX('.',@db1,1)+1,DATALENGTH(@db1)-CHARINDEX('.',@db1,1)))
IF CHARINDEX('.',@db2,1) <> 0
SET @db2=QUOTENAME(SUBSTRING(@db2,1, CHARINDEX('.',@db2,1)-1))+'.'+QUOTENAME(SUBSTRING(@db2, CHARINDEX('.',@db2,1)+1,DATALENGTH(@db2)-CHARINDEX('.',@db2,1)))
EXEC ('
SELECT * FROM
(SELECT * FROM '+ @db1 + '.' + @TableName +'
EXCEPT
SELECT * FROM '+ @db2 + '.' + @TableName +') T
CROSS JOIN (SELECT '''+@reason +' in '+@db2 +'.' + @TableName+''' Reason) T2
UNION ALL
SELECT * FROM
(SELECT * FROM '+ @db2 + '.' + @TableName +'
EXCEPT
SELECT * FROM '+ @db1 + '.' + @TableName +' ) T
CROSS JOIN (SELECT ''' + @reason + ' in ' + @db1 + '.' + @TableName + ''' Reason) T2')
Here I'm assuming that schema will be part of the TableName (which it should be if you're calling from sp_MSforeachtable). Also a tweak to skip sysdiagrams which gets picked up on my system (SQL Server 2008 Express).
Usage would be
sp_MSforeachtable "EXEC uspCompareTable dbname1, dbname2, '?'"