The Voynich Pipes

[MarcoP]

I have also found that there is an alternative version/transcription with “fixae” instead of “fixi”.

You are not allowed to view links. Register or Login to view.
You are not allowed to view links. Register or Login to view.

The first source simply refers to the Wiesenbach's article
The second one refers to the same Vat. Lat. 644.

The second one refers to Val. Lat. 644 in the footnote, saying that there it is "fixi". The main source of that transcription (with "fixae") is likely some other manuscript.

The You are not allowed to view links. Register or Login to view. refers to Reg. Lat. 1263 and Reg. Lat. 309, but apparently scans for these ms are not available.

But everyone can look and see that the MS says "fixi", not "fixe" or "fixae". While "e" in "rote" has a tail which probably serves for the abbreviation of "ae", in "fixi" it is clear "i", and not "e". Although medieval writers and scribes did not always exhibit 100% perfect Latin, I see no reason why one needs to imply "fixae". "Fixi" is the perfect of "figo", either 1st person singular active, or plural passive (see Verbix). There's no 1st or 2nd person here, so we turn to the plural 3rd person. "Rotae" is probably precisely that, because other declensions of "rota" ending with "ae" would be genitive or dative, which do not fit the context in which "crux" is also inflected.

So the reading of the 2nd line seems to mean that "thus <hoc> the wheels <rotae> of the Christ's cross <crucis Christi> have been fixed <fixi> in the clock <in orologio>".

"Rotae" and "fixi" do not agree. It should be "rotae fixae". E.g. the wheels have been fixed: rotae fixae [sunt]. "Fixi" cannot apply to a feminine noun.

I interpret “fixae” as a singular genitive linked with “crucis”.

So in this reading "fixae" is a noun? Which one?

Fixae cannot be a noun. I interpret "fixae" as a genitive, feminine, singular adjective (or past participle) applying to the genitive, feminine, singular noun "crucis". "fixae crucis" "of the cross fixed [to the wheel of the clock]".
As the English "fixed" that can be seen as an adjective or a form or the verb to fix, with the same meaning. 
In Latin, adjective and noun must agree in gender, number and case.