Reading frequency of an audio signal from Android device
There a few things missing here. Maybe too many questions for a comment, but maybe enough to help you see where it's going wrong. 

First of all, a 200mV peak to peak signal on 2.5V will give a range of 2.4V-2.6V, not 2.3V to 2.7V. Unless you mean it's 400mV p-p or 200mV amplitude. We'll assume you are dealing with a 400mV p-p 1kHz sine wave, since the other wouldn't work except to measure noise.

When you say a timer starts to measure the frequency, are you just seeing how long the signal is above your 2.61V reference? What are you expecting to find? A 314ns pulse from the comparator? Or are you just waiting for next rising edge of the comparator? What time resolution are you measuring at? What's your calculation?

Does the comparator have any hysteresis? If so, are you accounting for it?

Do you have any code for this project? Can you show it to us?

You should know that your method will only work for pure tone signals and it is very susceptible to noise. We don't know your ultimate application, so it's difficult to suggest alternatives.