Preloading an IIR Filter
This is a common problem, and has an easy solution. The following assumes you are using a cascade of second-order direct-form-1 sections.
 For a Butterworth highpass filter with a small ratio of Fcutoff to Fs, the numerator coefficients are close to [1 -2 1], and therefore the frequency response of the numerator by itself has a large attenuation at low frequencies. This is compensated by the gain of the recursive section (the poles). 
When a low-frequency sinusoidal signal is first applied, the input shift register (corresponding to the numerator) is not filled up until the 3rd clock cycle, and therefore the output of the numerator FIR may be large for the first 2 clock cycles, after which it becomes small. These initial large values get captured in the recursive section, and recirculate for some time until they die out.
So the simple solution is to delay the operation of the filter until the input shift register is filled with the first 3 samples.