It's a well-known issue reported here
viewtopic.php?f=4&t=901&start=0&hilit=chrome and here
viewtopic.php?f=4&t=565&p=3931&hilit=chrome#p3931My workaround is to use a hotkey like this:
Preferences > Hotkeys > Use the following hotkey to translate a word from clipboard: Ctrl + C + C
Then in Chrome select the text you want to look up and press Ctrl + C (which will copy it to the clipboard) and while still holding the Ctrl key press again "C". This way, "CTRL + C + C" will first copy the text to the clipboard and then execute the GoldenDict hotkey which looks for the text in the clipboard.
Personally, I open the main window and enter the term there rather than use the scan popup. It's more convenient.