The order of arguments does not matter.

Note that you're
not using
-r so you're passing 1 input folder, which is presumably excluded by your
--file-filter for some reason, and thus the
amc script is called with no input arguments.

The
amc script itself does accept folders as input, which it will then resolve for input files. But you want to pass an input folder, have
filebot itself resolve the files inside, apply your
--file-filter, and then pass the selected files onto your script.
tl;dr you're accidentally doing this:
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find /FileBot/Input -type f -maxdepth 1 -exec filebot -script fn:sysenv {} +
instead of this:
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find /FileBot/Input -type f -exec filebot -script fn:sysenv {} +

The
amc script itself doesn't like it if you use
-r because the
amc script itself likes to interpret the input and decide what to do with it, so it's typically used with a single input folder. But if you selected the files, and then pass them on as arguments, then it'll work with that input file set as is.
e.g. compare and contrast:
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filebot -script g:"println args" .
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filebot -script g:"println args" . -r
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filebot -script g:"println args" . -r --file-filter f.video
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filebot -script g:"println args" . -r --file-filter "folder.name =~ /.+/"
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filebot -script g:"println args" . -r --file-filter "true"

The key thing to note is that FileBot will interpret input arguments and resolve them to a list of file paths before a script is called, kinda like
find ... -exec filebot ... would collect files and then pass them as arguments when when
filebot is executed.
EDIT:
I think I know what got you confused:
If you do this, then you'll be passing in the current folder as input argument:
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filebot -script g:"println args" .
But if you do
--file-filter then you implicitly limit
filebot to
files within the given folder
(non-recursive without -r) that match your file filter expression, excluding subfolders and files within those subfolders:
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filebot -script g:"println args" . --file-filter true

So you need to use
-r recursive mode to apply your
--file-filter to either all files recursively in the given folder, or
-d folder mode to apply your
--file-filter to include / exclude sub-folders from the given folder. So without
-r or
-d if the folder passed as input contains no files and only folders, then that's zero file arguments, your file filter is never applied to anything, and zero file arguments are then passed to the script for processing.
EDIT 2:
If you're using the
amc script and just need regular expression based excludes, then you'll want to use the script-specific
--def ignore option, so the script itself can make the decision, and print log entires accordingly.