As SA said in his comment, this is too vague to discuss sensibly.
You can run into all sorts of problems with multi-threading - as you have discovered - without seeing the code you've used then I can't really comment further.
To be honest, 100,000 messages over 24hrs is not particularly high volume. It depends how large those messages are. Better approach is to find the optimal configuration of WebSphere for your requirements
This is where I refer you to the developer support resources provided, e.g.:
Configuring and tuning WebSphere MQ for performance on Windows and UNIX[
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The top 15 WebSphere MQ best practices[
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WebSphere MQ : IBM Support Portal[
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