Problem with installing biztalk MSI via BTSTASK ImportApp -GAC_MSIL is not updating correctly using powershell

Question

Program: Biztalk Server 2013
Server: 2012 Standard
issue: Installing via the BizTalk Server Administration Console using import MSI works fine, installing via powershell does not. Only a few of the items that should be updated in GAC_MSIL are being updated. The powershell script finishes with
Command succeeded with 0 errors, 0 warnings.
Looking through the powershell script's log file I see some warnings:
Warning: Schema "APPNAME.DataSetSchema1, [application name], Version=2.0.0.0, Culture=neutral, PublicKeyToken=4fbxxx03d" and a previously deployed schema "" have the same target namespace "http://schemas.datacontract.org/2004/07/System.Data". Target namespaces should be unique.
Warning: Assembly "[first assembly], Version=2.0.0.0, Culture=neutral, PublicKeyToken=9xxxxxx" depends on the following assemblies that must be installed in the Global Assembly Cache for runtime to succeed:
Assembly "[different assembly], Version=2.0.0.0, Culture=neutral, PublicKeyToken=8909xxxx"
Information: Deploy operation succeeded.
Information: Updating binding information.
The powershell snippets I'm using to turn on/ off and install the application are : 
#needed functions
[System.Reflection.Assembly]::LoadFrom("C:\Program Files (x86)\Microsoft BizTalk Server 2013\Developer Tools\Microsoft.BizTalk.ExplorerOM.dll")
function StopBTSApplication
param([string]$appName)
$exp = New-Object Microsoft.BizTalk.ExplorerOM.BtsCatalogExplorer
$exp.ConnectionString = Get-BTSConnectionString
$app = $exp.Applications[$appName]
if($app -eq $null)
Write-Host "Application " $appName " not found" -fore Red
else
if($app.Status -ne 2)
#full stop of application
$null = $app.Stop(63)
$null = $exp.SaveChanges()
Write-Host "Stopped application: " $appName
function StartBTSApplication
param([string]$appName)
$exp = New-Object Microsoft.BizTalk.ExplorerOM.BtsCatalogExplorer
$exp.ConnectionString = Get-BTSConnectionString
$app = $exp.Applications[$appName]
if($app -eq $null)
Write-Host "Application " $appName " not found" -fore Red
else
if($app.Status -eq "Stopped")
#full start of application
$null = $app.Start("StartAll")
$null = $exp.SaveChanges()
Write-Host "Started application: " $appName
}else{
write-host "App status is " $app.Status
function Get-BTSConnectionString
$group = Get-WmiObject MSBTS_GroupSetting -n root\MicrosoftBizTalkServer
$dbName = $group.MgmtDBName
$server = $group.MgmtDBServerName
[System.String]::Concat("server=", $server, ";database=", $dbName, ";Integrated Security=SSPI")
#end needed functions
$AppImInstalling = "name_of_app"
$MSIFolder = "folder where msi resides"
BTSTask ExportBindings /Destination:$localbindings /ApplicationName:$AppImInstalling
#stop biztalk to install resources correctly
StopBTSApplication($AppImInstalling)
Stop-service 'BTSSvc$BizTalkServerApplication'
Stop-service 'BTSSvc$BizTalkServerApplication32'
#Define msi file $localpackage = ($MSIFolder + "\"+$AppImInstalling +'.msi')
#install msi Write-Host "BTSTask ImportApp /Package:$localpackage /ApplicationName:$AppImInstalling /Overwrite "
BTSTask ImportApp /Package:$localpackage /ApplicationName:$AppImInstalling /Overwrite
### restore bindings from backup folder BTSTask ImportBindings /Source:$localbindings /ApplicationName:$AppImInstalling
# start biztalk
#Start-service 'BTSSvc$BizTalkServerApplication'
StartBTSApplication($AppImInstalling)
Start-service 'BTSSvc$BizTalkServerApplication'
Start-service 'BTSSvc$BizTalkServerApplication32'
Visible differences in the Admin console is that when I stop the application via the Gui only the main application I want is stopped.  When I stop the main application via powershell using the above functions a referenced application also shuts down
and that doesn't happen using the gui.   When starting the main application via the Gui it also fires up the host instances. When starting the main application up via powershell it doesn't start the host instances and I have to make separate calls to
start them again.

Answer 1

Update to this:
In the above script running a MSIEXEC install after importing the app updates the GAC_MSIL just fine!
# Do msi install$runMSI = "msiexec /i: $localpackage /qn "
Write-Host "MSI command to run :" $runMSI
&($runMSI )
I'm still very curious why the import app on the gui has a slightly different behavior. I wonder if the gui also just runs a msiexec in the background after the app imports.