My DD who just turned 8 is highly capable in math had a similar problem when she was 5. I did not teach her how to count much less add when she was little but the summer before kinder, I decided to go through 1 to 100 with her. She had taught herself how to count, add/subtract, simple multiplication and division, but for some reason could not count past 39..she would go from 38, 39 then 90 and miss out all the numbers between. It was bizarre and it took her a little while but ultimately it was some of sort of glitch that worked itself out. Now she is about 4 to 5 years ahead in math and has excellent algebraic reasoning, understands concepts extremely quickly and often times instinctively. She does have an odd habit of substituting numbers or words sometimes when she talks, but she is also verbally gifted and scored above 99.9% on expressive language on the WIAT so I have no idea what that is about.
DS8 has always been fluid with what numbers represent and are for. Based on his experience, the only red flag I see for your DS is - watch out for Common Core in early elementary! DS has broken pencils, shredded paper and bellowed in frustration at questions like "how did you figure out that 9+7 = 16?" In his words - "I didn't FIGURE IT OUT. It just IS!!!" (Visualize fist pounding table).
Suev, I wanted to say that this is EXACTLY how DD was in kinder and 1st grade and and ultimately the reason we pulled her out to homeschool. I agree, common core is good for most kids in expanding their understanding of the whys in mathematics, but horribly slow for mathy kids who have great math reasoning to begin with.
