Ford Vehicle Security System Alarm Upgrade to RKE

All,

Installed the Ford vehicle security system (VSS) upgrade to the remote keyless entry (RKE) in a 2007 Ford F-350 SuperDuty (diesel).  This is Ford part # 2W7Z-19A361-BA.  It is manufactured by CodeAlarm and is designed to use the RKE for activation/deactivation.

Installation was straightforward and all wiring information was provided by the manufacturer website at http://www.gemsen.com/ford.  Required approximately 10 connections including the starter interrupt.

Two odd operational issues that I'm at a loss for solving:

• Alarm initially operated as if all settings were set to default settings.  Upon entering programming mode for the first time, I noticed all settings were inverted.  That is, each setting read opposite of default as indicated by the dash-mounted LED.  Upon exiting programming mode, inverted settings were saved (as alarm did not function; one of the settings is whether security system is on or off).  Then, could not get back in to programming mode with door open (as instructions indicated and as originally completed); finally got back in but only when door was closed.  Needed to re-set all programming options to factory default once I got back in.  Inverted settings appear and are saved each time I enter and exit programming mode, unless I change them all to default before exit.
• One particular cycle of keypresses on the transmitter inhibits arming of the alarm.  If the doors are unlocked twice with the transmitter and then locked with the transmitter, alarm will not arm.  Need two presses of lock to get system to arm, OR need to have a door opened in between unlock and lock keypresses.  According to the instructions, one selection of lock on the transmitter should cause the system to arm after a 15 second delay.

I'm not sure if these are idiosyncrasies of the alarm unit itself or if they are a result of one of the connections I've made.  I've re-checked all connections at least twice and have ensured that jumpers on the unit are set correctly.  One thing on my plate is to try to disconnect the dome light output from the alarm as the truck has they enhanced security package (which controls the dome light with the RKE system).  Not sure if the double output may cause issues (at least one other installer I've spoken with does not make this connection).

Any thoughts or experience?

Thanks.