http://www.minecraftforum.net/forums/mapping-and-modding/minecraft-mods/2261180-voxelmap-1-8-1-7-10-1-6-4-a-minimap-and-worldmap?comment=522 - link to issue information with pictures. VoxelMap seems most affected by this issue, as seen by the pictures in the forum post. The author of VoxelMap, MamiyaOtaru, responded a post below the one linked above with possible solutions to the problem.

A waypoint - no issues.

A waypoint with Colored Lights mod installed. Only the text is garbled - the beam itself is faint but there.

Also, when Dynamic Lighting is enabled in the Options menu all maps render with a red overlay:
Without Colored Lights, no issue.

With Colored Lights, Minimap fullscreen and procedural maps all have red tint (untinted chunks hadn't been refreshed as I loaded the world without CLC at first).

These issues are fixed with VoxelMap release 1.5.4 - Dynamic Lighting and Waypoints function properly and I have found no issues with it outside of these.

Font is most likely borked still.

The only issue I see at all with it is the color of the waypoint beacon doesn't always show. I haven't seen issue with the font at all and I use three different texture packs (Invictus, Faithful & Sphax). I'll do more testing - I'm sorry for closing this prematurely.

Oh cool... he must have worked around what I was doing with the font then...