The Virgo medic component provides various logging interfaces and I wonder if Atomikos is binding to one of these. But if it was, I would expect the Atomikos log records to appear in serviceability/logs/log.log.
Perhaps the next step is to ask on the Atomikos forum what mechanism Atomikos uses to perform its logging.
You could also explore the wiring to the bundle(s) containing Atomikos and see if any obviously logging-related packages such as slf4j packages are imported by Atomikos and from where. You can explore the wiring most easily using the Equinox console and the ss, bundle, and packages commands. You can enable the Equinox console in Virgo as described in the User Guide - uncomment a line in the user region properties file in the config directory.
I don't know if or how you have converted Atomikos into bundle(s), but one question would be do these bundles have the necessary imports to enable logging to happen. For instance, if there was a missing import for a logging package, then Atomikos could be failing to log due to some kind of class loading error and it may not escalate such errors to console output.
To answer your question about the mechanics of Atomikos' logging: JDK logging by default, plus log4j if you put slf4j-log4j jars in your classpath. All my bundles have access to org.apache.log4j and org.apache.commons. So is this something that might be being bound?
Also, is there anyway from the Virgo side to determine if jta.properties is even being loaded from the root of the classpath?
Atomikos has an OSGi version, so I didn't do any conversion.
So Atomikos expects that the jta.properties file will always be in the root of the application's classpath. For a normal Java application, this wouldn't be a problem. But in the case of OSGi, there is a root classpath for the bundle, but does that equate to the root classpath of the application?
I wonder if Atomikos is looking at the Virgo root classpath instead of the bundle's?
Does Virgo provide any support for libraries that expect something in the root classpath?