A post-classical or quasi-Latin derivation of 'quandary' does seem appealing. In particular, I'm inclined toward understanding it as a closed compound from quando or quanda (-a in spurious agreement with the feminine; bothboth in the sense of 'at what time', but the first in an adverbial sensetime?') and res (feminine), with the closed compound used in the sense of 'a persistent state or condition of questioning "when?"'. Such a proposal is at least no more fanciful than the suggestion that quando was mistaken for the first person singular of a verb with the infinitive 'quandare' meaning 'to question when' or 'to question what time'.
Some attestations that might seem to support those more fanciful derivations include--if only the meaning corresponded--include these:
Opposing any appeal of fanciful Latin etymologies, however, is that the earliest attested use, by Foxe in the 1563 edition of Acts and Monuments, is of the form 'quandarie', as shown next, in Etymology 2.
Alongside that opposition, it is noteworthy that in 1886 Oliphant, a keen and knowledgable student of the changes from Middle English to the 'new English', accepts a derivation from wandrethe proposed by Wedgwood in 1873, and designates turbatio as the Latin equivalent.
A problem with positing a Latin etymology for 'quandary' is that, while a number of likely routes for such a derivation suggest themselves to the imaginative, no solid evidence can be found. For example, Foxe's original use of 'quandarie' in the 1563 edition of Acts and Monuments seems to have been predicated on the use of turbatio in the original Latin edition of Acts (the text of which is not available to me, but was possibly a secondary source for Oliphant).
Note also that Foxe was a Latinist; the 1563 edition of Acts represented a revision and expansion from the original Latin version into vernacular English.
Additionally, although 'quandare' does appear with some regularity in the 17th century, and occasionally in the 16th, the earlier forms from the 16th include 'quandarie' and 'quandary'. This hints that a Latin derivation may have been supposed, on speculative grounds, by later authors.