I had this issue for a long time - on a relatively-new iMac running on Wifi using USB external storage for recordings. I took the following measures:
-replaced my external USB drive - unlikely for you, but try using an external storage. SSDs do eventually fail in cases of heavy read/write use.
-Trimmed down other processes running on the machine. For example, backup programs, system utilities, etc. I particularly trimmed my backup sessions to the middle of the night when there would be no recording.
-turned off the commercial skip feature (if this is done after endcoding, this likely didn't help at all)
-updated to HDHomerun latest firmware (i believe it does NOT auto-update)
-power cycle my router (poor firmware on routers can make routine reboots a necessity!)
-cleared streaming cache and turned off all experimental features
Also, watch you activity monitor during an encoding operation. Maybe something has changed in your system and now your resources are being taxed by the encoding process.
If I think of other measures I took to improve encode quality I will come back and post again.