They look like 2 different searches, are you 100% certain you copied the correct GREP codes into the Find box - the Change to is also completely different?
Yes. In first image the point two is reproduced in InDesign Find/Replace window. The text was:
1. Copied from PDF - the result is that one
2. Saved the PDF as Word and copied the query from MS Word file. Same result.
3. Imported the MS Word file into InDesign and by drag and drop I set teh Find what: but it looks the same though in all three cases they were looking OK on documents. meaning even when I imported Word file into InDesign, in the text frame the sequence was correct but not when I pasted it into Find/Replace window.
hope any of these make sense to you.
I wouldn't say copying from Word or PDF is reliable.
Try putting them into Notepad first (or TextEdit)
It looks like this is a case of the parnetheses being switched and then mirrored in Hebrew. There's a discussion about this from earlier this week with regard to typesetting Arabic and Importing text from Word.
I'm guessing here that you don't type or read Hebrew, or really do much in the way of handling RTL languages. The rules that govern which-way-the-parentheses-point differ from place to place, here. Notably, the GREP query window doesn't use the same layout rules as your InDesign document. If my guess is correct, I'd suggest to you to simply rekey the GREP query, and copy/paste individual Hebrew characters from the PDF into the GREP query, without stopping in Word or in your ID layout.
(Or perhaps Save As Plain Text from Acrobat?)