Hello. I am using a custom programmer based on the ArduinoISP. After two hours of puzzlement, I figured out that selecting the programmer from the tools menu has NO EFFECT. The solution I found was to delete this line from boards.txt:
Apparently this line overrides any settings the user selects from the GUI programmer menu. I am not sure if this problem occurs for other boards, but this is the one I was having an issue with. After commenting out that line I can select any programmer and they work.
I’m assuming you are uploading using the programmer rather than burning the bootloader. By default the Arduino AVR Boards use serial upload using the bootloader and indeed the Tools > Programmer selection has no effect on that operation, however it’s not a bug, that’s the intended behavior. To upload with an ISP you will want to do Sketch > Upload Using Programmer or hold shift while clicking the Upload button. When you removed that line from boards.txt you cause Upload to do Upload Using Programmer.
Thanks, you were right. I restored the boards.txt file, and it works with the "upload with programmer" button. I feel like an idiot now!
There is no need to feel like an idiot. You are learning about this stuff, that is good, and the forum is where to ask questions. This type of question may get more answers if put in the Microcontrollers section of the forum. If you're going to program Pro Minis most often via a programmer instead of FTDI upload using the bootloader, it is fine to modify the boards.txt file to your liking or to create a custom boards.txt entry that meets your needs. You could also change the fuse BOOTRST to run the sketch directly, instead of trying to run the bootloader. The bootloader is erased anyway when you upload a sketch with a programmer. The fuses are set only when you do the Burn Bootloader function of the IDE, or if you run avrdude on the command line to set the fuse using a programmer.