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In general, PuTTY's terminal handles the Alt modifier key by prefixing the Escape character to whatever it would have sent for the key you pressed with Alt. For example, Alt + b sends ESC and then b.
For most function and arrow keys, in most modes, this works just the same. For example, in PuTTY's default function key mode (labelled "ESC[n~"), the F6 key sends ESC followed by the text "[17~", and if you press Alt + F6, then you get an extra ESC, so two copies of the ESC character followed by "[17~".
However, the "Xterm 216+" function key mode incorporates modifier text into the escape sequence indicating whether Alt was pressed: on a modern xterm, F6 sends ESC [17~ and Alt + F6 sends ESC [17;3~, where the extra parameter 3 indicates a combination of modifier keys (in a confusing way) that can include any of Ctrl, Shift or Alt.
Therefore, PuTTY should not also send an extra prefix ESC: in this mode, Alt + F6 should send just ESC [17;3~, not ESC ESC [17;3~.
In 0.81 and before, on the Windows platform, it sent the latter.