As you mentioned, this effect does not change the relative correlation between all variables and this is expected behavior. The following is noted in the documentation:
"Biplot imposes a sign convention, forcing the element with largest magnitude in each column of coefs to be positive. This flips some of the vectors in coefs to the opposite direction, but often makes the plot easier to read. Interpretation of the plot is unaffected, because changing the sign of a coefficient vector does not change its meaning."