Not sure if you got all this sorted out but here is what I have been testing as a config for the ALR-9900+
factorysettings
timeZone=-3
dhcp=off
AutoMode=OFF
Clear TagList
AcqG2Cycles=8
AcqG2Q=5
AcquireMode = Inventory
AntennaSequence=0 1 2 3
AutoAction = Acquire
AutoFalseOutput=-1
AutoFalsePause = 0
AutoMode = OFF
AutoMode = ON
AutoModeReset
AutoStartPause = 0
AutoStartTrigger = 0,0
AutoStopPause = 0
AutoStopTimer=-1
AutoTrueOutput=-1
AutoTruePause = 0
AutoWaitOutput=-1
AutoWorkOutput=-1
Function = Reader
NotifyFormat = Text
NotifyHeader=OFF
NotifyInclude = Tags
NotifyKeepAliveTime = 30
NotifyMode = OFF
NotifyMode = OFF
NotifyQueueLimit = 1000
NotifyRetryCount = -1
NotifyRetryPause = 10
NotifyTrigger = OFF
PersistTime = -1
RFModulation = STD
TagListAntennaCombine=OFF
TagStreamFormat=Text
TagStreamMode=ON
TagType = 16
AutoMode=ON
Save
Also make sure you don't have any macro enabled: MacroList
If you have a default Macro "default" it will always revert back to the maro setting! (run "macrodel default" to remove it)