wine-1.2.3 vs wine-1.0.1

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I am using wine to run a windows executable from a java program under linux (via java ProcessBuilder, jdk1.6.0_13) and collect the output (via InputStreamReader/BufferedReader).  The java program was working with wine-1.0.1 (under Debian 4), but is broken after migration to CentOS 6.2 with wine-1.2.3.  For certain input data to the windows executable, wine-1.2.3 now generates a Program Error and only partial output gets read back into java.  (For the offending input data, on the linux command line however, wine-1.2.3 could generate the file with the complete output from the windows executable).

In several test cases, the mis-behavior occurs when more output is generated.

Is it possible that some program settings are different from wine-1.0.1 to wine-1.2.3 that could cause this behavior? Perhaps there may be verbs in winetricks that can 'flush the output' notwithstanding the condition giving the Program Error?

Any suggestions/pointers/help would be greatly appreciated.
 

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