7683B ALS not injecting properly into 7890A

Windows XP ?  Wow....  In Windows Explorer under the subdirectory that is your, for example, Run_Check_Method.M ...there is a file -  acqmeth.txt.  Please copy/paste the contents to your reply.  One setpoint is "Sample Washes," where the ALS takes sample out of the vial into the syringe and then squirts it out into the waste vial. That is followed with "Sample Pumps" where it pumps the syringe plunger up and down in the sample to eliminate bubbles.  Then the system waits for everything to go Ready, then pulls up the typically 1 µL into the syringe, the entire syringe assembly lifts up and then injects into the inlet in a very short less than a few tenths of a second.

The simplest thing to try is to shutdown MSD Chemstation, start up Agilent GCMS Configuration and create a second instrument. That creates new default methods.  Then start up Instrument 2, load Default.M, edit entire method, and see how it goes.

Here's the contents of the acqmeth.txt of the method I was initially trying to run: 

INSTRUMENT CONTROL PARAMETERS: ANALYTICAL 1 S 251
-----------------------------------------------------

C:\MSDCHEM\1\METHODS\alsTEST.M
Fri Jul 12 09:18:13 2024

Control Information
------- -----------

Sample Inlet : GC
Injection Source : Manual
Mass Spectrometer : Enabled

Oven
Oven On
Equilibration Time 0.5 min
Oven Program
140 degrees C for 10 min

Post Run Temperature 140 degrees C

Front Injector

Back Inlet SS
Heater On 280 °C
Pressure On 16.017 psi
Total Flow On 66.226 mL/min
Septum Purge Flow On 3 mL/min
Mode Split
Gas Saver On 20 mL/min After 2 min
Split Ratio 100 :1
Split Flow 62.6 mL/min
Injection Pulse Pressure 10 psi Until 0.75 min

Thermal Aux 2 {MSD Transfer Line}
Heater On
Temperature Program
280 degrees C for 0 min

Column #1
Agilent 19091Z-231: 325 °C: 15 m x 250 µm x 1 µm
HP-1 Methyl Siloxane: 2450.48206
Out: Vacuum

Column #2
Agilent 112-8867: 250 °C: 60 m x 250 µm x 0.2 µm
HP-88: 4745.43467
In: Back SS Inlet He
Out: Vacuum

Column #3
450 °C: 25 m x 320 µm x 0 µm

Column #4
450 °C: 25 m x 320 µm x 0 µm

Column #5
450 °C: 25 m x 320 µm x 0 µm

Column #6
450 °C: 25 m x 320 µm x 0 µm

Signals
Test Plot Save Off
Test Plot Save Off
Test Plot Save Off
Test Plot Save Off

MS ACQUISITION PARAMETERS

General Information
------- -----------

Tune File : atune.u
Acquistion Mode : SIM

MS Information
-- -----------

Solvent Delay : 8.00 min

EM Absolute : False
EM Offset : 0
Resulting EM Voltage : 1882.4

[Sim Parameters]

GROUP 1
Group ID : 1
Resolution : Low
Plot 1 Ion : 31.00
Ions/Dwell In Group ( Mass, Dwell)
( 31.00, 100)

[MSZones]

MS Source : 230 C maximum 250 C
MS Quad : 150 C maximum 200 C

END OF MS ACQUISITION PARAMETERS

TUNE PARAMETERS for SN: 
-----------------------------

Trace Ion Detection is OFF.

EMISSION : 34.610
ENERGY : 69.922
REPELLER : 25.264
IONFOCUS : 82.565
ENTRANCE_LE : 19.000
EMVOLTS : 1882.353
AMUGAIN : 2102.000
AMUOFFSET : 119.000
FILAMENT : 1.000
DCPOLARITY : 0.000
ENTLENSOFFS : 16.816
MASSGAIN : -617.000
MASSOFFSET : -34.000

END OF TUNE PARAMETERS
------------------------------------

END OF INSTRUMENT CONTROL PARAMETERS
------------------------------------

I've just set up the second method to the same parameters as the method I was previously attempting this with. After multiple attempts, the ALS and sample tray are not seen using the new default methods, and when attempting to load methods from the previous setup all 5 methods that I tried had the same failure: they would continue to inject into the sample bottle rather than into the inlet. 

Line 8:  Injection Source:  Manual.   It must be set to ALS

In MSD Chemstation it will look very similar to this, but do "Edit Entire Method" and on this screen, select GC ALS, then OK, continue editing the method, and then save it as a new name, like 22Jul2024 with ALS.M  or something, and try it.

Isothermal GC run, simple. Pulsed split injection that is lower than the starting pressure?   There are two columns configured, one is  no IN to vacuum. Column 2 is Back inlet to Vacuum, I don't see column flow listed? Are you doing constant pressure at 16 psi or the recommended constant flow ?    16 psi for this configuration is 1.378 ml/min, just a tiny bit higher than optimum, but it will work.

SIM only one ion, 31?   Are you only looking for methanol?   If there is any oxygen in the system it may have trouble with big 32 ion interfering with your 31 ion...

Line 8:  Injection Source:  Manual.   It must be set to ALS

In MSD Chemstation it will look very similar to this, but do "Edit Entire Method" and on this screen, select GC ALS, then OK, continue editing the method, and then save it as a new name, like 22Jul2024 with ALS.M  or something, and try it.

Isothermal GC run, simple. Pulsed split injection that is lower than the starting pressure?   There are two columns configured, one is  no IN to vacuum. Column 2 is Back inlet to Vacuum, I don't see column flow listed? Are you doing constant pressure at 16 psi or the recommended constant flow ?    16 psi for this configuration is 1.378 ml/min, just a tiny bit higher than optimum, but it will work.

SIM only one ion, 31?   Are you only looking for methanol?   If there is any oxygen in the system it may have trouble with big 32 ion interfering with your 31 ion...

This method was a bit weird, it's pretty old and I'm not sure who created it other than that it was designed specifically to test the ALS system so I figured that would be my best way to test for any sort of functionality. I did your recommended changes and it was still having the same error until I was going through some more troubleshooting and saw that the REMOTE connection between the GC-MS was not ready. I removed the REMOTE cable on the MS side and magically our ALS started injecting properly! We have a light on the vacuum indicator that says the MS isn't ready but I can't see why that would impact it as it's been like this in the maintenance logs for at least 10 years and didn't hinder the readiness of the system before now. Especially since it's for the Micro-Ion gauge and that's optional from what I've seen. I'm still doing more testing but I can't fully discern if the error is in the remote cable itself stopping the "Ready" state of the system, or if it's something on the GC or MS side.