Mirth Running Old JAR File Code

This is really driving me crazy. No matter what I do, it seems that Mirth (1.8.2) is running an older version of my JAR file; I know because of various signs, like:

I can't call any functions
Information logged is not showing up in the logs
Changed log messages are not changed in the log files
Files that were once created and written to in code, but no longer touched by code, are still being created and written

I've tried everything I can think of to make this work. It was working at one point, but now it seems like it's no longer being updated. My process to integrate my changes into Mirth are:

Run an ant script to build the JAR file
Copy the JAR file to \lib\custom
Restart the Mirth service (via Mirth administrator)

I've tried restarting (Mirth service via Services, Java, computer) -- to no avail. I know my JAR file is correct, because I've decompiled it (to make sure it has the latest code) and hashed it (to compare to the hash of the ant-built JAR) -- it is correct and the code is there; it's just not being run.

I'm at wit's end; this occurs infrequently but completely blocks me from developing.

Edit: I also know that my code is correct, because when I run unit tests, it generates the right files and calls the right functions and logs the right information. Only Mirth seems to "not get it."

And my classes are very simple; simple one-argument constructors and a few public methods that return various data. Nothing complex, no nested classes/JARs/dependencies.

Edit: I even deleted my custom JAR file and restarted Mirth, and it's still running my code. Awesome :/ I've added a bounty for this question. I suspect the JAR is cached somewhere (even though they deny it on the Mirth forums) and that cache needs to be cleaned out somehow (although why restarting the Mirth service and my PC doesn't do it is beyond me).

I've also killed all instances of Java (and rebooted my computer), so that makes it highly unlikely that the JVM is caching the JAR somewhere.

I tried reinstalling Mirth. For some reason, it had my custom channel when I booted the administrator for the first time; and infuriatingly, it's still running the old JAR, even though I've updated it with the new one in lib\custom.

Solution

I ended up solving this with a combination of actions:

Uninstalling Mirth and Java, and then reinstalling.
I also removed all Java installations except one (one JDK and one JRE).
I stopped Mirth when you copying my JAR. Stop Mirth, copy, and restart; don't try to copy on a live installation. It may or may not pick up your updated JAR depending on if it's loaded into a JVM or not.

This combination of steps seemed to work. Prior to this, I had 3-4 JREs installed (and two JDKs) and I was copying (successfully, according to Windows 7) the JARs while Mirth was running. It's working now!