1. I've noted that if I just run reply without arguments and in its shell type "use mymodule" it just works fine.
2. If I run any installed module (reply -M Data::Dumper) works fine

Here is header of my simple module:

    #!/usr/bin/env perl
    package Wik;

    use v5.20.2;
    use strict;
    use warnings;
    use open qw/:std :utf8/;
    use utf8;

    use MediaWiki::Bot qw(:constants);
    use Data::Dumper;
    use YAML::Tiny;
    use Path::Tiny qw(path);
    use Getopt::Long;
    use HTTP::Date;
    use Pod::Usage;
    use URI::Escape;

    require Exporter;
    our $VERSION = 0.2;
    our @ISA     = qw(Exporter);
    our @EXPORT  = qw(login savepages updatepages);
[download]

Hello guiwp,

Just on an off-chance, your rcfile isn't this module, right? Because, auto loading modules and other meta configuration are to go into your rcfile. This rcfile is actually an INI Config file and my rcfile looks like this:

script_line1 = use strict
script_line2 = use warnings
script_line3 = use 5.018001

[Interrupt]
[FancyPrompt]
[DataDumper]
[Colors]
[ReadLine]
[Hints]
[Packages]
default_package = SMS::Send
[LexicalPersistence]
[ResultCache]
[Autocomplete::Packages]
[Autocomplete::Lexicals]
[Autocomplete::Functions]
[Autocomplete::Globals]
[Autocomplete::Methods]
[Autocomplete::Commands]
[download]

Take a look at Reply::Config and Config::INI::Reader::Ordered. If you've already covered it, great! If not, just something to cross out. :-)