I don't think I've ever looked at this before; this is ridiculous and strange and wonderful.

• Allows insertion / epenthesis of segments (0 > e / #_sC)
• Logging to file + console
• Improved logging, including line number and file name for the script in which the error was found.
• Now attempts to log all compilation errors encountered in all loaded scripts before quitting
• Added some clarifications to the manual where users indicated some sections were unclear.

https://github.com/samanthamccabe/toolbox-sca/releases/tag/0.6.0

That's really weird. toolbox-sca-0.5.0.jar is in that folder right? Everything should be right there. it's very strange that it couldn't find it. You could try also running it manually with

java -jar toolbox-sca-0.5.0.jar pq_rules.rule

which is basically what the batch file does. Sorry you are having these problems, I've tested this quite extensively, so I really hope I didn't miss something.