Agar, and in particular its component agarose, may sequester essential nutrients. We have recently provided evidence that growth of strains mutated in genes encoding for zinc transportres is impaired on plates, unless plates are supplemnted with zinc

If you tell the gene name, would be easier to guess why. If the gene function is related with cell envelope or even pili, you may have some growth alterations  in solid phase, at the end of the day a bacterial colony is a type of biofilm. Many alteration in biofilm do not show any apparent phenotype in liquid culture. Hope this help.

Agar, and in particular its component agarose, may sequester essential nutrients. We have recently provided evidence that growth of strains mutated in genes encoding for zinc transportres is impaired on plates, unless plates are supplemnted with zinc

Just brainstorming:

The nutrient supplying surface in solid growth is 2D and nutrients get depleted, in liquid it's 3D and shaking the culture nutrients are renewed constantly. So I would bet you have a deficiency in metabolism but not a loss of function phenotype.

Hope this spreads ideas...

What is the strain in question? Are the media components the same in the plates and the liquid media? Sometimes your agar plate bacteria due to surface area, do grow at a different rate compared to being agitated and incubated for growth.

I totally agree with Andrea Battistoni.

Maybe you have any inhibitors in solid medium culture, I can advice you to use the same medium in solid and liquid form (like LB) if it is if it is compatible with this E.Coli strain.

Sincerely, I am not a microbiologist but I hope you can find help in my answer :)

An important clue as to the reason for the difference in growth on solid vs. liquid medium would be if you were able to see micro-colonies on the solid medium.  If micro-colonies form, a likely mechanism for the difference would be the local depletion of a micro-nutrient, or the accumulation of a toxic metabolite.  In other words, inhibition due to the spacial structure imposed by the medium.  If you don't even see tiny micro-colonies, it is more likely that the addition of agar to your liquid broth has changed it chemically in a way that is preventing growth.  You could try to use a different solidifying agent such as Gelrite.  The standard formulation of M9 is not my favorite minimal medium for E. coli, it tends to contain too little iron.  If the agar is sequestering cations, this could very well be your problem.

It may be due to overgrowth of wild-type revertants or compensatory mutants in liquid culture, but not on solid media. Is the gene-deletion mutant selected for with an antibiotic? If it is, then in liquid media the antibiotic is effectively being diluted out as bacteria grows, allowing any revertants to grow and over-take mutants which are less fit. This can happen on solid media but at a slower rate due to slower growth dynamics on solid media. You could check whether this is happening by plating out some liquid culture (no selection for revertants, with selection for compensatory mutants) and carrying out colony PCR on 20 or so colonies. 

There can be many reasons as pointed out by others. But, one major reason could be that in liquid culture, the cells get more oxygen compared to growth in solid medium. This happens to a big group of e coli knockout strains. Just do this (my suggestion to you): try to perform a growth experiment without any shaking in liquid media i.e. standing culture experiment. You might pick up growth defects as you see in solid media.

Difficult to give any definitive answer without information on the nutritional defect itself. Some nutrients are used up quite slowly and depending on the details of your subculturing techniques their may be sufficient residual supplies for many generation's growth. I observed this with sulfonamide, which inhibits folate metabolism in E. coli. Sulfonamide sensitive strains formed colonies in the presence of sulfonamide, presumably relying on residual folate in the cell suspension, but they could not be subcultured on the same medium.