Mapnik rendering giving odd results as tiles but not as single file

I'm trying to render some data in a .osm file, mainly for debugging purposes at this stage, but it will become a proper overlay.

I'm using this generate_image.py script and defining a simple XML stylesheet, which results in this .png file (screenshotted as follows), which all looks correct (and the .osm file is routable in OSRM too) :

However, if I use this generate_tiles.py script to generate a tile tree (instead of the single .png file as above), only fragments of the ways are shown, in an inconsistent and fragmented form, shown here zoomed into level 12 or so:

The OSRM routing when zoomed in at this level does follow those line fragments exactly, but obviously goes further than the extent of each fragment.

It's not a browser caching issue - creating a fresh tileset, and creating an incognito instance (which bypasses the cache) gives the same. When I zoom in, different fragments of the ways are shown.

Is this likely to be a projection issue? As far as I can see, it's all set to Google Mercator.

Any other ideas what might be causing this problem? I've been fiddling with this for a day or two now and stuck!