Jaxer has configuration settings that allow logging levels be adjusted. Here are some of the settings that you can turn on/off when trouble shooting a problem (Assuming windows platform here).

mod_jaxer (applicable only if apache is configured talking to Jaxer):
This is the module that apache uses talking to Jaxer. The loggings generated by this module are in your apache log (“Aptana Jaxer\logs\apache_error.log” if using the shipped apache server).
To generate extensive loggings, go to your httpd.conf (“Aptana Jaxer\Apache22\conf\httpd.conf” if using the shipped apache server.), change the LogLevel to debug, and restart apache.
LogLevel debug

JaxerManager:
JaxerManager manages the individual Jaxers. It is the bridge between the webserver connector (eg mod_jaxer) and jaxer. JaxerManager writes logs in the same file as Jaxer does. The log file is jaxer.log under “Aptana Jaxer\logs” if you are using the standalone Jaxer install.
You can turn on trace either from the JaxerManager command line (--trace=on) when you start JaxerManager or issue a (set trace on) command through its command port. You can use the utility program tellJaxerManager to do it.
From command line:
JaxerManager –trace=on
After JaxerManager has started:
tellJaxerManager “set trace on”
To turn off the trace,
From command line:
JaxerManager –trace=off
After JaxerManager has started:
tellJaxerManager “set trace off”

Jaxer:
Jaxer is the main process that does the work. It has a few settings that control various logging levels. All Jaxer logs go to the same log file as JaxerManager.

Turn on protocol dumping:
When it is turned on, Jaxer logs all network traffic between it and the webserver connector. The setting is in defaults\pref\Jaxer_prefs.js under the jaxer folder (Aptana Jaxer\jaxer\defaults\pref\Jaxer_prefs.js if using the shipped apache server.).
pref("Jaxer.dev.DumpProtocol", true);
The change requires restarting jaxer. To turn it off,
pref("Jaxer.dev.DumpProtocol", false);

Other Jaxer settings:
In the same Jaxer_prefs.js file, the following settings can be turned on (true) or off (false). Note that these settings control individual levels. Thus to get the maximum loggings, you should setting all of them to true.
pref("Jaxer.CoreTrace.EnableWarning", true);
pref("Jaxer.CoreTrace.EnableInfo", true);
pref("Jaxer.CoreTrace.EnableDebug", true);
pref("Jaxer.CoreTrace.EnableTrace", true);
The configLog.js (under “Aptana Jaxer\local_jaxer\conf” if you are using the standalone Jaxer install) contains additional settings mainly controlling the loggings for server-side javascript execution. You can edit the function() body to adjust the logging levels. Your settings here override the settings in jaxer\framework\configLog.js.