I do not know how you are entering your Greek text, but it is not being entered with the correct character set. That fact that it is "\f1| is irrelavent. I know there has been a lot of talk on the forums about the proper tags for e-Sword. And that is all fine and good, except it is not relevant to what you see in T4. Your Greek text may be \f34! T4 will switch font based on character specifications at the time it creates a module, and if it sees a font that is fcharset161, then it become \f1 for greek. In the file you posted, the greek is indeed \f1 (but again - that is irrelavent), the problem is the fcharset if 0. This is one time where editing the RTF may help. Change it to fcharset161, then build your module. But note!!! Other characters may be tagged \f1. In your file. the second mark changed after editing the RTF and had to be deleted and re-entered.
I drove it around the block again and the superscripts look great... but the greek font isn't displaying as the e-sword default TITUS. I expanded the sample file so it was easier to see. I have all the greek tagged with \f1, everything else is \f0.
The T4 Greek Keyboard, enters Greek character with the correct fcharset. Copying and pasting from some documents will not always have the correct fcharset. I do not have any hard and fast rules to say when copy and paste from other documents works.