Properties of a PDF that Affect Direct Text Copying to Other Programs?

I am using a program that Acrobat Pro XI does not convert its files to (e.g. word). Therefore, I select & copy sentences from PDFs and paste them into this program. Most of the time, copying special characters like the greek letter psi from a PDF shows up as “Y” when I paste it into the other program. However, there are some PDFs that actually paste psi correctly.
What’s interesting to note is that these different properties are observed in similar PDFs. For example, my professor posted lecture notes as PDFs: notes from lecture 4 allow me to copy&paste all special characters properly, while lecture 7 notes do not, even though they look very similar as documents.
Can anybody think of any properties/settings that may be different between the two PDFs? Even if I cannot fix the problem, at the very least I might be able to predict which ones allow direct copying.
Any help would be greatly appreciated.
Note:  "Y" vs. "Psi" registration is independent of the program I paste into.  Word follows the exact same copying trend as my other other program

Not sure why you cannot convert to WORD in AA XI. Just use File>Save As and select the WORD option.
As to the psi, it may be that the font used in one of the files was different and you do not have it on your computer, so the copy used the closest version it could find. You can use ctrl-D to check the fonts in the system. Since you mentioned psi, do not expect the conversion of mathematics to WORD to be done well or at all. It may be the fonts used were from MathType and you would need the MathType fonts on your machine in that case. It would be a lot easier if we could look at the PDFs, but they may not be available for general posting. If you like, you could try a private message and setup to send the files by e-mail to review.

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