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Thanks for responding EJP but it seems the upgrade we did to the piece of software either corrupted or did something strange to the cacerts file. We found a copy of the same file from before the upgrade, copied it over the current one and hey presto, everything started working as normal....Not sure what was wrong as we've done the upgrade a few times in our testing environments and we've never seen it before.
I originally copied the unlimited strength files into the JRE but didn't think to put it in the JDK. Not sure if the JDK is installed.