The $4 boards come with a bootloadable program, meaning that if you press the button while powering it up, it will allow you to load a new program, but that program has to be bootloadable as well so you can reprogram it again.
The $4 programmer for example is bootloadable so you can reprogram it later for other uses.
So, if I write a hex file that is bootloadable but also overrides the EXTCLK I'm not sure if it will stay bootloadable, I have to experiment a little with that to make sure I don't override your bootloader.
Using the $4 programmer or the Pioneer with a modified KitProg, allows you to program the chips without the need of them having a bootloadable image.
I did test my $4 programmer with a new hex file and it worked fine. Maybe you had some wires crossed or something like that
From the protoboard to the SSOP I had:
P2.0 connected to P3.2 (SWDIO)
P2.1 connected to P3.3 (SWCLK)
P2.4 connected to XRES
ground and power.
If it's programming the blue LED on the protoboard should be flickering while it programs and verifies, if you don't see flickering then something is wrong and enters the bootloader mode. You need to power it off and on again to start the programmer again.
Edit: I just tried by trying different combinations of disconnection or not paired up to the right pin, and the $4 programmer just starts to blink (no flickering just a steady blink at 3 per second) that means something is not hooked up right.
So my question to you is, do you need it bootloadable image, or are you going to use another $4 board to program it?