It's very, very easy for a modder to accidentally cause a chunk to load in vanilla minecraft.
In fact, this happens without mods too, just not as regularly. For example, villages cause it when checking if doors exist, and mob spawning causes it if a low view distance is set.

Why? When a mod, or minecraft, tries to get a block in a world, it asks "get me the block at these coordinates". In Vanilla, this tries to get the chunk that block is in, then returns the block. However, if the chunk isn't loaded, it loads the chunk. After this, the chunk will then never be unloaded, and can can be considered to be "orphaned", as it is not associated with any players.
ChickenChunks tries to improve performance by unloading these chunks, so they don't stay loaded forever.

A modder can avoid loading chunks in this way, but it means they have to check if a chunk is loaded every time they get a block which can be very tedious, so most don't bother.

Orphaned chunks cause lag in two ways:

• Lag spike from loading the chunk, single time (multiple times with chunk GC)

• Overall worse performance from having the chunk and any tile entities/entities in it loaded

Unfortunately, chunk GC will make performance worse in many cases, as the chunk will be reloaded immediately. It's best to set a high chunk GC period, which you have done.

Loading chunks accidentally when retrieving blocks/etc. can be fixed globally by using an alternative server implementation which allows this to be disabled, for example MCPC , TT, or both. This doesn't work in all situations, as some mods depend on this behaviour. Portals will no longer load chunks on player login, and IC2 nuclear reactors which are across chunk boundaries will not work. I don't know of any other issues related to disabling this, but they probably do exist.

edit: Just to note, I have simplified this a bit. Many operations can cause chunk loading, not just getting the block at a location. Trying to find the tile entitiy at a location, the lighting of a location. Basically, anything that retrieves information stored in a chunk.