Sometimers I think this is because the genre of music is one that is not yet woven into one's heart. Once the genre and its formulas, or an individual piece, is in the heart, the rhythm is unconsciously obvious.But I also have noticed that transcribed music is sometimes pretty badly laid out, for the PULSE of the piece. In the spirituals, for instance, some versions have started a measure off (to begin the piece) with a note that, in another version, is set up in the measures as a pickup note. SO the whole piece staggers on, an accent off the true feel of the piece.
Make sense?
In that latter case, unless one knows the piece or the tricks of that particular genre, it can be hard to "hear" the piece through the dots until one has internally translated it back to its proper feel. Then the dots, however badly set up across the measure breaks, make sense. Think of it like learning to read a foreign language from a font missing its tails... letters from a penpal, typed on a damaged typewriter. After awhile your mind fills in the tails, because in English you know they must be there, so you put them where needed in the new language. The measures adjust themselves in your mind, like that.
And sometimes the way someone writes the notes down fits for the math of the notes, but not for the phrasing. What might show on the page as a tied pair of notes, adding up to one long note, actually is sounded as two separate notes.... or on a series of notes, the eighth note tied in is in the wrong place in the sequence, compared to the sound....
Then there are the conventions of rhythm of a genre, hard to quantify into notes without using 32nds and 64ths... shuffle-bowing I think cannot be transcribed perfectly, because the little hitrches in time are so slight that writing them down would be a pain in the ass. The spirituals have this too-- if you look in some fiddle books you will see a footnote for some pieces that what is written as a straightforward rhythm is actually meant to be played as though certain notes are dotted and others halved.
Anyhow, IMO when you get into the intricacies of dotted sixteenths you need all the visual cues you can get, to de-goof a piece you may never have heard well enough to memorize.
Me, I like to hear them first and then see what they become once I get 'em going in my head. THEN maybe I am ready for notes, and to adapt them to MY arrangement, whether I ever write it down or not.
~Susan