I found that it tended to misalign the trigger point from the transient some of the time. At worst it would trigger on something that seemed entirely arbitrary. There was something 'hands on' about manual splicing that I always dug. Sure, that's a self-serving excuse, and you can probably see right through it, but it's all I have to hold onto, man
it sounds like you're really just missing out on a critical stage of BD... auditing the automatic results, using varying zooms.
on the first audit pass you just look for false and missing beat triggers... zoom in to where you can view a few to several bars at a time, depending on the density of the playing, and delete and add them quickly as you run through that pass... this goes very fast normally if you have chosen the best detection analysis algorithm and sensitivity to start with... just scroll through using your scroll wheel and add and delete as necessary... very quick. make certain you have beat triggers on every transient that should have one, and no "falsies" remaining.
Then zoom a bit further in for the second pass.. make sure that "Show Trigger Time" is checked in the Region Separation pane, and that the radial button for Sub-Beats is indicated.... now scroll-wheel through and make sure the trigger times... the beat/sub-beat that BD will move each transient to, or closer to, depending on the Strength setting you have chosen in the Region Conform pane... is correct for each beat trigger. This goes much quicker than you'd think, especially once you're used to what the subdivisions will read as for each type of rhythm. Correct each one as necessary by simply double-clicking on the beat trigger and entering the correct value. Your success here will depend highly upon your remembering to Capture Selection and choose the appropriate subdivision in the "Contains:" drop-down in the Selection Pane for each section you work on.
to get tweaky you can add a third step to the audit process: zoom very far in and move through each trigger via the Scroll Next button in BD... and manually moving beat triggers to fine-tune their location on the transient as desired.
then just make sure you've set a Trigger Pad of around 10-20 ms in the Region Separation pane and hit Separate. move to the Region Conform pane, set your desired Strength, and hit conform... if you've taken Audit step #2 everything should move to the correct location, or closer to it as per your Strength selection. then move to the Edit Smoothing pane, make sure the Fill and Crossfade radial button is indicated, and set a Crossfade time for one half the trigger pad value you set earlier in the Separation pane. Hit Smooth.
Boom! done... no "bad splices".