I don't know the 8085, so these are just wild ideas.
Does it do the same with the CTC set to a different address.
Does the system work okay with, say, a PIO instead of the CTC, perhaps set to the CTC's address.
Does it make any difference removing the CTC modules oscillator signal from the CTC inputs.
Actually, I can't think of any scenario that accounts for the problem so these really are just complete guesses.
Steve