There would be several improvements for your code. But let's focus on the timeout. Below extract from the help for the DAQmx Read VI should share some light :
number of samples per channel specifies the number of samples
to read. If you leave this input unwired or set it to -1, NI-DAQmx determines
how many samples to read based on if the task acquires samples continuously or
acquires a finite number of samples.
If the task acquires samples
continuously and you set this input to -1, this VI reads all the samples
currently available in the buffer.
If the task acquires a finite number
of samples and you set this input to -1, the VI waits for the task to acquire
all requested samples, then reads those samples.
Therefore, in your case, the counter read waits for 1000 samples but with a timeout of 0.
There are several possible solutions but what I recommend is to use an Array Size function to compute the number of values of the analog read. By wiring this number to the number of samples per channel input of the counter read you will read the exact same number of samples for both tasks in each iteration of the loop.
Don't hesitate to post again if you should need further help.
