I don't use the SMART Board software myself, but it looks like you have three options...
1) Create a batch file like srochford's (or mine) and run it on each computer (either manually or automatically via another method). The command line switches shown in red below will run the cleanup utility without any user interaction. Once it has finished, the shutdown command will reboot the computer.
Board95Cleanup.cmd
Code:
@echo off
setlocal enabledelayedexpansion
set SCRIPTDIR=%~dp0
set SCRIPTDIR=%SCRIPTDIR:~0,-1%
start "" /wait "%SCRIPTDIR%\board95cleanup.exe" /s /v"/qb"
shutdown -r -t 10 -f
2) Create a CC3 package which runs the EXE (and subsequently the MSI contained within).

SMART CleanUp Utility v9.5.ini
Code:
[Package]
Description=SMART CleanUp Utility v9.5
Version=1.0.0.0
OS=5.WS,6.WS
EXEFile=Board95Cleanup.exe
AddCommand=/s /v"/qb"
3) Create a CC3 package which runs the MSI you extracted from your %TEMP% folder. The ISSETUPDRIVEN=1 command should prevent the MSI (created with InstallShield
) from complaining.

SMART CleanUp Utility v9.5.ini
Code:
[Package]
Description=SMART CleanUp Utility v9.5
Version=1.0.0.0
OS=5.WS,6.WS
WIPackage=Board95Cleanup.msi
AddCommand=ISSETUPDRIVEN=1
Hope that helps?