Well I decided to download and try out the latest and greatest host software and firmware.
I set forth to do the normal changes, but couldn't for the life of me figure out why the host would crash each time I wanted to jog an axis. It was rather stupid of me, I cleaned the 5D gecode -> Interpreter and reinstalled the files, again, and again. Finally after posting on the forum, I tried something else out, delete the applet directory, as this is where a fresh compile of the code goes.
It worked, powered up the machine, then the host software. Doing it this way instead of the other way around which I had been doing just fine for the old firmware worked. I hate to think wat will happen when I use the bluetooth at the end of the build cycle, as I did have it going before quite reliably.
I also upgraded my Java version, I hadn't done it because of frequent host crashes, however another recent post suggested editing the repRap.bat and change "Java" to "C:\Program files\Java\bin\java.exe" or where ever it is located.
That fixed that long outstanding issue.
Still have to restart my computer after exiting from a crash or even a normal exit.
It is still unknown if this is a problem with Java, or its implementation in the host, my feeling its the host, but what I just don't know.
Lastly I found that with the atest firmware it wants to home too quickly for my flatbed scanner, this I believe is due to the acceleration in the firmware, sadly because it is desgned for equal stepper motors all round, which I don't, I want this turned off anyways, which I have done now in the firmware configuration file.
Forwards and nwards to the next problem, redesigning the Y axis, as folding the internal flap didn't work out, I did this at work when I wasn't even thinking, I was just too tired and not with it.
Which was ok, as I had to wait about 15 minutes between charge cycles when fixing units anyway, which had charging faults.
Using this method for the Y axis, adds strength and alows for an easy way to attach a bar so that it can reach an endstop if I need to, plus affixing the belt onto it as well.