In the README file there is an explanation of the 95th percentile problems.  Basically, the more you (mean) average the data -- by going from daily, to weekly, to monthly etc -- the lower your perceived 95th percentile will appear, since the peaks of data have been smoothed out.  The amount of inaccuracy depends on your data, how many brief unusual spikes it contained.
For example, if there were a couple of 5-min spikes every 2 hours, then you would have a big difference between monthly and daily.  If you have a more constant pattern, then there would be little if any difference.  You need some statistical analysis knowledge to understand the underlying reasons, and I tried to give that up 10 years ago 
One possibility is to make big extensions to your MRTG .rrd file.  If you extend the daily RRA to a whole month, then the 95th percentile calculations *should* spot this and pull out the data in the best resolution possible.  This will take longer to calculate, but will be much more accurate.  I will check the code to see if this will indeed be the case.
Steve