I have lots of ACA gpx files and have not had any issues overall.
This may be an obvious question but in BaseCamp (BC) is the Activity Profile setting set to Direct? The Activity Profile (typically a drop down menu at top of the BC page) will allow you to set the "activity", i.e. Automobile, Bicycling, Hiking, DIRECT, etc. If on direct, it will only do direct line-of-site "routing" to the next waypoint.
Since BC does is not on the GPS device, no alerts are given since you are at a desk. You must also select your Activity Profile on your GPS device typically. You don't mention the device you have but the setting is typically under Settings. I personally select the option "Ask Every Time" (or similar) as if I am on a rail trail, the device keeps trying to re-route me to a road so then I will purposely select Direct, otherwise, Automobile.
Another reason is that for some odd Garmin reason (not ACA as it does it on routes I create too),I have found that the device seems to work better if you Transfer (Send to Device) the data in Direct mode. For some reason, occasionally it will not allow the route to be changed in the device, i.e. Invert, if you send it in something other than Direct. Garmin is clueless but since it is not an every time or even frequent, they ignore it.
Anyway, without trying to sound rude, you probably are missing something because others have not had an issue. Keeping playing around with it and you will hopefully figure it out.
Worst case, if you private message me, we can set up a time to talk and I will try to walk you through it.
Hope you work it out as the routing does help. Tailwinds, John