99 Silverado not downshifting w/rem. star

Just installed a remote start/alarm in my 99 silverado.  I used a dei 555L for the passlock II for the remote start.  2 problems I have noticed. 

1. When you use the remote start to start the vehicle and then get in to drive, the trans. seems to stay in high gear.......I can manually drop down into 3rd or 2nd but it will not down shift while in drive.  If I start the truck with out the remote start, just with the key the trans. shifts fine up and down. 

2. Service engine soon light is on....is this something to do with the above problem?

One more question while I've got your attention....I'd like to install window modules.  My alarm has a 2nd ch. out put and a 3rd ch. output...both prog. with a .8, 10, or 30 second pulse.  .8 will not work of course, but 10 seconds is too long.  It takes about 5 to 6 seconds to roll up or down.  Will this in turn dammage my window motors in they continue to turn for the extra 4 or 5 seconds?

Any help would be great!

Mark

Shade Tree Installer

Would it be a straight connection from the alarm, splice off from  orig. ignition from the alarm?  Or should I use a relay from the ignition? 

Thanks for the help

mark

I checked my rs and it did have a 2nd ign., so I connected it to the white wire.  I disconnected the battery before connecting to the white wire for about 1 hour.  Then connected the white wire to the 2nd ign. from the rs.  The engine now shifts like it should, but the service engine soon light is still on.  Any ideas on this?

Thanks

Mark

Service engine soon light went off today.  So everything is working like it should.  Thanks

for your help.

Mark