When I remove the Upper Jumper on the rear of the module, the full scale range doesn't change from 100nSec to 1uSec as the manual implies

Full Scale Ranges were defined by the way the module was configured prior to shipping.
Four user selectable time ranges are provided in a given configuration.  All channels need not have the same scale factors. Custom ranges are available when ordering.  

Standard Configuration
 Alternate Configuration
Range
 Resolution
  Range
 Resolution
100 nSec Range
 25 pSec
 1 uSec Range
 0.25 nSec
200 nSec Range
 50 pSec
 2 uSec Range
0.50 nSec
400 nSec Range
 100 pSec
 4 uSec Range
 1.0 nSec
800 nSec Range
 200 pSec
 8 uSec Range
 2.0 nSec

All the jumpers on J44 (the upper jumper on the rear panel) are read only jumpers.
The upper most jumper in the rear of the module lets the module know if you want the nanosecond ranges, or the microsecond ranges when performing internal tests.  This combined with the next four Range Select Jumpers tells the module how many clock cycles to wait between the START and STOP pulses during the 1/3 [F(25) A(1)] or 2/3  [F(25) A(2)] Internal Tests.

This could have been hard wired, but some modules with custom ranges, may want to test the channels with both short and long Start to Stop time intervals.
Example:  Channels 1 - 8 (100ns Standard Configuration),   Channels 9 - 16 (1us Alternate Configuration)

F(25) A(1)   [The 1/3 test]  with Jumper IN:   Start to Stop is about 45ns
Channels 1 - 8 read  about 1200 counts ,    Channels 9 - 16 read around 180 counts

F(25) A(1)  [The 1/3 test] with Jumper OUT: Start to Stop is about 350ns
Channels 1 - 8 read  full scale 4095 counts ,    Channels 9 - 16 read about 1200 counts

J-44 Jumper
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