Ok, here's some advice: boil the program and example code down as small as possible but keep it working.

Something like this:

<myxml xmlns:xs='bla'>
<xs:complexType name="AlternateSecurityIdentification1">
<xs:sequence>
<xs:element name="Id" type="Max35Text"/>
<xs:choice>
<xs:element name="DmstIdSrc" type="CountryCode"/>
<xs:element name="PrtryIdSrc" type="Max35Text"/>
</xs:choice>
</xs:sequence>
</xs:complexType>
</myxml>
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Will parse.

Also:

foreach my $complex(keys %{$data->{'xs:complexType'}}) {
print $complex;
my $seq = $data->{'xs:complexType'}->{$complex}->{'xs:sequence'};
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Is probably easier written as:

foreach my $subseq (values %{$data->{'xs:complexType'}}) {
  my $seq = $subseq->{'xs:sequence'};
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Then print()/Dump() the data you've got at various stages and see which line(s) are causing problems.