The "lost founder" problem is when someone who is a founder, and has founder equity, is no longer participating in a startup.  Anyone who has experienced the "lost founder" problem knows that it can be very negative for a startup.  Many people think that because they were part of early brainstorming work or university developments, that they are also a "founder." 

Founders of companies are the people that are going to BUILD the company.  The reason that people become lost founders are myriad.  Sometimes the startup takes too long to "get rolling", sometimes they're unwilling to work for cheap or free during the pre-investor or pre-revenue phase, sometimes they lose interest or have a falling out with the other founder(s).  For whatever reason, there's no talent being contributed, but there is a chunk of equity that is held by the lost founder.

This is of grave concern to investors.  They want founders equity in the hands of those people who are contributing on a day to day basis!  Although many entrepreneurs have the misguided notion that investors exist to "take their company", in reality sophisticated investors have a very clear notion of how much equity (at a minimum) must be in the hands of founders at each round of investment.  If it is too low (and they set their guidelines based on long experience), the investors know that the founders can become un-motivated and walk away.   So when you take the "precious pool" of founder's equity and split off a half or a third of it and essentially "throw it away" on a lost founder, it hurts the investors because it hurts the remaining founders that hurts the company. 

See also the post on Issues with Founders and Buy-Sell agreements which talks about how to deal with a founder who is withdrawing from the company (hint - always have a Buy-Sell agreement!)