When troubleshooting configuration problems, posting the actual files rather than screenshots is far more effective. I realize it's not always possible, but since you are a new Forum member (welcome !) I thought I'd mention it.
Why did you change the controller in the first place ? Was the original controller an SLC-5/04, or an SLC-5/03 ? Your answers are not clear on that.
The good news is that there's no firmware revision or hardware change that would shut down the communications port when you enter run mode.
When you download a program to an SLC family controller, the last thing the RSLogix 500 software does is check the Communications channel configurations and compare them to the current settings in RSLinx. If these are different, the software presents a warning letting you know you *may* lose communications on the current or the other channel of the controller.
It is absolutely vital that you pay attention to those messages when they appear.
The label "KF3" on your DF1 Full Duplex driver is unusual. It appears that you might have been using "DF1 to DH+" or "DF1 to DH485" pass-through communications, which requires you to select a different Device Type in your RSLinx DF1 Full Duplex driver, as well as requiring specific Status bit settings in the controller.
Do you recall "going online" with the other DH+ connected controllers while plugged into the serial port of this SLC ?
Check the configuration in RSLinx for the "known good" controller to see what the "Device Type" is. Examine the Processor Status -> Chan.1 tab in RSLogix 500 to see if any of the passthrough configuration bits are set.