MSI

there is no point in convertting a .exe to a special .msi. there is no benifit. sure your library has a .exe blocker but they have that for a reason. .msi is primarly used as a installer for microsoft products. even wikipedia agrees with me that its a WINDOWS INSTALLER format. http://en.wikipedia.org/wiki/.msi

the .msi format is also propriatary.

Edit found this information out via my computer...

Windows ® Installer. V 3.01.4001.5512

msiexec /Option [Optional Parameter]

Install Options
| /i>
Installs or configures a product
/a
Administrative install - Installs a product on the network
/j [/t ] [/g ]
Advertises a product - m to all users, u to current user
| /x>
Uninstalls the product
Display Options
/quiet
Quiet mode, no user interaction
/passive
Unattended mode - progress bar only
/q[n|b|r|f]
Sets user interface level
n - No UI
b - Basic UI
r - Reduced UI
f - Full UI (default)
/help
Help information
Restart Options
/norestart
Do not restart after the installation is complete
/promptrestart
Prompts the user for restart if necessary
/forcerestart
Always restart the computer after installation
Logging Options
/l[i|w|e|a|r|u|c|m|o|p|v|x|+|!|*]
i - Status messages
w - Nonfatal warnings
e - All error messages
a - Start up of actions
r - Action-specific records
u - User requests
c - Initial UI parameters
m - Out-of-memory or fatal exit information
o - Out-of-disk-space messages
p - Terminal properties
v - Verbose output
x - Extra debugging information
+ - Append to existing log file
! - Flush each line to the log
* - Log all information, except for v and x options
/log
Equivalent of /l*
Update Options
/update [;Update2.msp]
Applies update(s)
/uninstall [;Update2.msp] /package
Remove update(s) for a product
Repair Options
/f[p|e|c|m|s|o|d|a|u|v]
Repairs a product
p - only if file is missing
o - if file is missing or an older version is installed (default)
e - if file is missing or an equal or older version is installed
d - if file is missing or a different version is installed
c - if file is missing or checksum does not match the calculated value
a - forces all files to be reinstalled
u - all required user-specific registry entries (default)
m - all required computer-specific registry entries (default)
s - all existing shortcuts (default)
v - runs from source and recaches local package
Setting Public Properties
[PROPERTY=PropertyValue]

Consult the Windows ® Installer SDK for additional documentation on the
command line syntax.

Copyright © Microsoft Corporation. All rights reserved.
Portions of this software are based in part on the work of the Independent JPEG Group.

As stated numerous times above, .msi is an installer format, not an executable format. It is made for installing programs, not actually running them.

If you also look on the converter's site, it states "A free tool to quickly convert .exe setup application to a msi package".

Notice the words ".exe setup application", as in installer-type executable, not all executables.

Ok, I can tell you why what you are trying is working:
The .msi file bundles the .exe into it because it can't tell the difference between an application named setup.exe or an installer named runme.exe. When you run the .msi files you are making, all you are doing is telling msiexec to configure nothing on the system and then run the .exe.

Have you actually tried running one of your converted .exes at the library? I'm just interested to know if msiexec would be a workaround for the exe blocker since it actually runs the .exe within the .msi file.

Unfortunately though, making a portable app into a single .exe would be at best difficult for most apps, impossible for others. The reason portable apps work as portable as they are is because of the AppNamePortable.exe file. It would also have to be done on a per-app basis, which would be very time consuming.

I am wondering what would happen though if you changed the AppNamePortable.exe and Appname.exe both to .msi, and changed the relevant .ini entries to call AppName.msi instead of AppName.exe.