If you check the Template Toolkit manual, you'll notice:

Multiple templates may be specified as a reference to a list. Each is processed in the order defined.

my $template = Template->new({
    PRE_PROCESS  => [ 'config', 'header' ],
    POST_PROCESS => 'footer',
};
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and

Alternately, multiple template may be specified as a single string, delimited by ':'. This delimiter string can be changed via the DELIMITER option.

my $template = Template->new({
    PRE_PROCESS  => 'config:header',
    POST_PROCESS => 'footer',
};
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So, judging by your issue and the way that you have set multiple PRE_PROCESS templates, I think this will fix your problem.