I'm running the latest git (on my armel box - HTS Tvheadend 4.1-2378 as of right now).
Here's a screenshot of some of the services, I recently mapped (just to test for you).
http://i.imgur.com/vuILs1b.png
Tvheadend correctly uses the LCN set by the provider (notice the number gap between 5 USA & ITV4).
http://i.imgur.com/wPSlmQH.png
By default if a service does not have an LCN set Tvheadend will use the (lowest) next available number. What you're seeing might be because the provider has (re)moved the channel & left a dummy service to inform users (using a standard box) that they need to re-tune in order to receive it again. Sometimes these dummy services have LCNs and sometimes they won't. Here in the UK most STBs will either ignore services with no LCN (and hide them from the user), or place them in the 800+ channel range.
If you can confirm that Tvheadend is using the incorrect LCN (Local channel number value is set in services) & the service is active (play it in VLC) open an issue.