Can you try below signature?
<MultipleInstance>
<Iterator export="true" name="INSTALL_PATH">
<FindFilePathEx name="MYFILE.txt"/>
</Iterator>
<Instance>
<Variable export="false" name="file_read">
<ReadFile path="$(INSTALL_PATH)MYFILE.txt"/>
</Variable>
<Variable name="IS_INSTALLED">
<Contains inputString="$(file_read)" position="contains" searchedString="MYAPP_version=1.3"/>
</Variable>
<Condition withVariable="IS_INSTALLED">
<Action do="SKIP" onValue="false"/>
</Condition>
</Instance>
</MultipleInstance>
Check below link since it contains a post to debug the signature issue