As suggested, programmers that connect to the serial port (but aren't serial port programmers) tend to be troublesome - because they often rely on the serial port exceeding the RS232 standard.
However, another possibility is the config fuse settings, have you enabled the internal oscillator in the 16F88's?. If you have, you may not be able to enter programming mode anymore with a crude programmer - because you have to enter programming mode BEFORE the oscillator can start running, this requires either switching Vdd, or being able to ground MCLR to reset the device.