User690216013 posted
In classic mode, js files are typically handled by static file handler of IIS. But in integrated mode, any managed handler of your application can process them and lead to issues if they should never touch those files.
Therefore, you have to carefully analyze your handler mappings. Because it might not be a good idea to post your IIS settings online, you might open a support case via
http://support.microsoft.com and further discuss with the support professionals.