strange issue. when i launch isearh and want to paste text into it, after pressing C-s the paste (S-insert) always pastes the text to the current edited buffer and not the isearch window. has anyone come across anything like this?
There is no "strange issue" here - just a misunderstanding. The behavior you see is by design.
What you call the "isearch window" is in reality not a window, and it does not display a buffer. It is just the echo area, which is an output area for showing messages to the user. It is not an input area.
If you try to use an ordinary yank (paste) command during Isearch then the text gets yanked to whichever buffer and window are currently selected. That's what you're seeing when you use
Isearch reads individual characters that you type (wherever you type them), and it echoes them to the echo area so you can see that it has added them to the current search string. It does not use that area where you see the "prompt" and search string as the minibuffer - it does not read input from there.
You can yank (paste) text that you copy from elsewhere to Isearch, to be appended to the search string. For that, you need to use one of the special Isearch yank commands, such as
isearch-yank-kill (bound to
C-y during Isearch). (You could, if you wanted, bind
isearch-mode-map to the same command.)
And you can use
isearch-edit-string) to interrupt Isearch to edit the current search string, using the minibuffer. There (in the minibuffer) you can yank (paste) text normally - the minibuffer allows general editing.