I believe that the battery monitor bases its readings off battery voltage. My wild guess is that the 6V batteries aren’t putting out 12.75 volts the monitor is expecting. Have you measured your battery connection with a voltmeter? This should be your first step.
http://www.sandiegorvandgolfcartbatt...batteries.html
Or maybe you hooked the 6V batteries in parallel like your 12V batteries were, instead of serial.
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-Scott, DW, DG, DB, and DD
2011 Passport 2590BH
2009 Ford F150 SuperCrew F
X4 5.4L w/Max Tow