Thanks for providing those details. I'm going to ask you to back up and do some clarifying.
Exactly which model of PLC-5/40 is this ? There were the uncommon PLC-5/40VME and 5/40L, the very common PLC-5/40B (with four total DH+/RIO ports), and the PLC-5/40E with Ethernet.
Which port are you connecting to the DH+ network ?
How are you connecting your computer to the DH+ network ? Are you using a true RS-232 to DH+ interface like the 1770-KF2, or a 1784-PKTX or -PCMCIA, or a modern USB to DH+ interface (1784-U2DHP) ?
You mentioned at the start that you have "configured the DIP switches". When the PLC-5/40 is configured to use Channel 1A as DH+ (very common, and by default) then it gets its Station Number and Data Rate from the settings of Switch 1. This is illustrated on page E-2 of the
PLC-5 Enhanced and Ethernet User Manual.
The functionality of each channel of a PLC-5/40 is determined in the user program. If Channel 1B, 2A, or 2B is configured for DH+, then the Station Number and the Data Rate come from the user program, not from the DIP switches.
It is possible that your user program has Channel 1A configured for a RIO scanner, so once the program has been downloaded it can't communicate on DH+. I think that's consistent with the Channel 1A indicator LED flashing (RIO scanner with no slave devices) and being unable to communicate with Channel 1A.
It's been a decade or more since I touched a PLC-5 so this is largely from memory (with a quick refresher from the User Manual).