I doubt that it's related to Timer1.
I use Timer1 all the time and have never had a similar problem.
I would suspect LVP (Low Voltage Programming) RB4.
What do you have attached to RB4?
It should be connected to something that provides a LOW voltage on power-up.
When the chip is erased, LVP is automatically enabled.
If the pin is left floating or has a HIGH level on the pin, the chip will not program anymore.
Placing a resistor from RB4 to ground will solve the problem...
If that is the problem.
Added: Are you using an external crystal for Timer1?
T1CON = %00001010 enables Timer1's External oscillator, and those pins are also the clk and data pins for ICSP.
The programmer may have problems if there's a crystal attached.
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