I do not know where to begin. First: It is not DPI, it's PPI. DPI is printing, PPI is Screen. Second: Not one screen today probably has 96 DPI. Most have more. Stop forcing this one. Third: If I need to manually write into Xorg.conf about the dpi/ppi, accept my values.
Thanks for listening. If someone has questions about ppi/dpi and what the heck it is, please ask me openly.
I am sorry I don't know which component does this mess.
The global DPI value is a historical relic - it cannot have meaning in a world
with multiple outputs as part of the same logical display. Actual measurements
need to come via the RandR extension that can provide info for each output
*** This bug has been marked as a duplicate of bug 41115 ***