B2B Integration server memory problems

In one of the webMethods Integration servers that we administer, some time ago, after months of flawless operation, random memory errors started to occur.
It usually has the form of one particular structure tnMessage (that was by bitesToString, stringToDocument, documentToRecord created from bizdoc/Content) having disappeared from the pipeline. Depending on the exact time of the disappearance, we get different flow errors.
From the forum I got a tip that it might be related to too many files open in WmRepository2, and cleaning files from WmRepository2 might solve this issue.
Applying this tip did not give positive results.
Remarkable is that in an other identical B2B Trading Networks Integration server the error never occurs. Both servers are on the same machine (Sun Solaris), one is installed in /opt/webMethods with 5555 as primary port, the other in /opt2/webMethods with 8555 as primary port. Both use the same java_root but are runtime separate java processes of course.
The error occurs in the /opt2/webMethods on port 8555 only. Concurrency of processes is excluded as cause of the problem.
By trial and error I found that by having savePipelineToFile as one of the first service steps, before the bytesToString, the error does not occur. but as soon as savePipelineToFile is disabled or removed, the error does occur. So I use this now as a workaround.