<<<why the discrepancy between the 90% and 75% figures>>>>
This difference is irrelevant at a cellular level. There are so many independent variables controlling mRNA and protein levels that a 15% difference means little. What is important is that both drop. Remember that both mRNA and protein have half lives and, although they often reflect each other in trend, ie. rapid turnover or slow turnover, they are independent of each other. And then there are is the whole issue of whether that 15% difference is statistically significant. The PR does not tell us how reliable the measurements are.
Be happy that the levels are close and are moving in the same direction.