Personally, debugging is just done by putting print statements in the code to test my assumptions. You have already done this. I would help you debug it but you would have to provide a runnable program that exhibits the undesirable behaviour. I tried to reproduce your bug with the code you have provided by doing the following

I copied

 show_amend_userorderroute()

removed the sub declaration, commented out the sql and put

use Tk;
my $window = MainWindow->new();
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at the beginning, changed

my $frame = $mainmenu->Toplevel(-title => 'Amend User',);
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to

my $frame = $window->Toplevel(-title => 'Amend User',);
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and put

MainLoop();
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at the end. I get

Tk::Error: Undefined subroutine 
&main::process_amend_userorderroute called at C:
\Documents and Settings\blm\Desktop\test2.pl line 37.
 Tk callback for .toplevel.button
 Tk::__ANON__ at C:/Perl/site/lib/Tk.pm line 247
 Tk::Button::butUp at C:/Perl/site/lib/Tk/Button.pm line 111
 <ButtonRelease-1>
 (command bound to event)
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This means the program tried to run the desired routine and I was unsuccessful in reproducing your bug. (I didn't bother copying and pasting the process_amend_userorderroute to my test code)