I have some apps in same server without problem.
My Alias lines are similar to yours, bat have some diferences.
You can try the way that I do, perhaps works for you:
Alias /my_app_1 "C:/my_app_1"
Alias /my_app_2 "C:/my_app_2"
If don't work, try this:
<Directory "C:/my_app_1">
Options FollowSymLinks ExecCGI
AllowOverride None
Order allow,deny
Allow from all
DirectoryIndex hyper_app.dll
</Directory>
Alias /my_app_1 "C:/my_app_1"
<Directory "C:/my_app_2">
Options FollowSymLinks ExecCGI
AllowOverride None
Order allow,deny
Allow from all
DirectoryIndex hyper_app.dll
</Directory>
Alias /my_app_2 "C:/my_app_2"
I hope this helps.