First, make sure you've got warnings enabled everywhere, it'll help you catch typos and other accidents (see also Use strict and warnings):

$ perl -wMstrict -e '$Module::configvar=0; if($Module::confgivar=1)
    { print "<$Module::configvar>\n"; }'
Found = in conditional, should be == at -e line 1.
Name "Module::confgivar" used only once: possible typo at -e line 1.
<0>
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If that doesn't help, you can trace when the variable gets set, put the following debug code at the top of your program, above use Module; and anything else that may make use of $Module::configvar. It will show you exactly when values are stored in the variable.

BEGIN {
    package LoggingScalar;
    require Tie::Scalar;
    our @ISA = 'Tie::StdScalar';
    use Carp 'cluck';
    sub STORE { cluck "STORE"; shift->SUPER::STORE(@_) }
    tie $Module::configvar, 'LoggingScalar';
}
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