Thanks for the replies acannell & Fastest1
After posting this thread I did manage to get a hold of Roberto, not so easy with time difference in mind. So after yet another sleepless night I left that conversation a little clearer as well as confusing the both of us lol. My machine is apparently of rogue spec :/ it has an NT40 spindle arrangement (only offered with R8 or NT30), a 5HP motor (only offered with a 3HP) and somehow has Windows 95 running in the background (these are a DOS based machine). As far as we could establish over the phone it is a Dyna unit in spite of these oddities.
Suggestions put forth by Roberto:
Make my own RS232 cable following the configuration set out in the help menu. An off the shelf cable MIGHT not have the correct config and could cause the breakdown in communications. Also I could remove the hdd and install it into a desktop as a slave unit to copy the files. To run the actual program from a desktop has many boundaries involved such as 32 bit only & only certain versions of windows are compatible.
Check in the PLC section of the machine for the functionality of the limit switches. This showed that the Y axis was always active tho physically all components test OK. Also the fact that the warnings only appear after I have homed the machine and am trying to run a program would suggest the limits are working fine. This does remind me of another issue I have with the machine that could actually be linked. On the Z axis sending it all the way up actually jams the machine requiring me to remove the front cover and manually reverse the ballscrew back into operating range. This strongly suggests an out of bounds issue in the parameters, something I am not too eager to mess with. On a side note, DAMN those limit switches are expensive!
As far as the reverse operation issue goes the only suggestion he could make was the possibility of corrupt software. He also suggested I could check over the settings but without the machines serial number they have no way of giving me the exact settings for this machine as they are all individual in setup from factory.
From this point I think my next steps are: 1. install HDD into desktop and get a backup made 2. make an RS232 cable 3. consider replacing the limit switches (for something a little easier on the pocket of course) & 4. use the damn thing manually if all else fails
Thanks again guys for your help and I will keep you posted with my progress. Maybe one day my woes will become somebody elses savior.