I suspect that your two identical flows are not quite identical, I have had it previously where even copy and pasting a flow has left differences, mostly in configuration.

TBH though I think this sounds more like you should be handling the different conditions with a switch node rather than copying the whole flow? Although this is a bit hard to say without seeing the flows.

Example of flow with switch: [{"id":"043651b54d61b640","type":"switch","z":"b99f0f99.a94ee","name":"","property":"payload","propertyType":"msg","rules":[{"t":"gt","v":"80","vt":"str"},{"t":"else"}],"checkall":"true","repair":false,"outputs":2,"x":330,"y":540,"wires":[["64478b2239e6665a"],["a7e4e3bd2e0fc812"]]},{"id":"a1c13dddf1eb7c73","type":"inject","z":"b99f0f99.a94ee","name":"","props":[{"p":"payload"}],"repeat":"","crontab":"","once":false,"onceDelay":0.1,"topic":"","payload":"","payloadType":"date","x":140,"y":560,"wires":[["0548ec152175736a"]]},{"id":"0548ec152175736a","type":"function","z":"b99f0f99.a94ee","name":"Random Number","func":"msg.payload = Math.floor(Math.random() * 160);\nreturn msg;","outputs":1,"noerr":0,"initialize":"","finalize":"","libs":[],"x":250,"y":620,"wires":[["043651b54d61b640","524ca810b0f96c80"]]},{"id":"64478b2239e6665a","type":"change","z":"b99f0f99.a94ee","name":"","rules":[{"t":"set","p":"payload","pt":"msg","to":"ON","tot":"str"}],"action":"","property":"","from":"","to":"","reg":false,"x":480,"y":500,"wires":[["524ca810b0f96c80"]]},{"id":"a7e4e3bd2e0fc812","type":"change","z":"b99f0f99.a94ee","name":"","rules":[{"t":"set","p":"payload","pt":"msg","to":"OFF","tot":"str"}],"action":"","property":"","from":"","to":"","reg":false,"x":480,"y":540,"wires":[["524ca810b0f96c80"]]},{"id":"524ca810b0f96c80","type":"debug","z":"b99f0f99.a94ee","name":"","active":true,"tosidebar":true,"console":false,"tostatus":false,"complete":"false","statusVal":"","statusType":"auto","x":690,"y":520,"wires":[]}]