I have been developing multiple Perl+GUI tools in my company. I also faced similar issues like you when packaging for Windows. After a lots of research, Past 2 years I have been using "PerlApp" - Active State PDK. PerlAPP is a nice utility from Active State to convert perl scripts to Windows EXEs.
I have following configuration,
1. OS: Windows 7 x64 bit
2. Perl: Active Perl 5.16 x32 bit version, I need to create exes for x
+86 & x64 beside, I have not yet got a situation to force me to move o
+n x64 perl.
3. GTK2: Get Gtk2 and other essential pre built perl packages from Rep
4. Glade: Get windows version exe of Glade 3.8.1 (3.14 version is not
+working good in windows) from Gtk website - This is to develop GUIs a
+nd load from code.
5. That is it - You can use perl app to convert your Gtk2-perl script
6. Note: sisyphusion's repository builds Gtk2 with using GCC Libs. So
+you need include c:\Perl\site\bin\libgcc_sis_452.dll and c:\Perl\site
+\bin\libgcc_x86_470.dll in perl App project as a "Bound Files" with a
+uto extract on startup option. So these libs will be available to you
+r exe for linking.
7. Note: You should also include any resource files, Ex: Pix map image
+s / glade file as a "Bound Files" and in your code you need to extrac
+t before using.
8. Have a look my perl Gtk2 project: http://code.google.com/p/saaral-s
+oft-search-spider/ , Browse for code and see how I handle perl APP bo
+und files. Also there is an exe (perlApp created) , you can play with
+ it to see how Perl+Gtk2 exe behaves.