A few things to check/ask. There can be any number of explanations or things to look at:
1. How did the levels of the full factorial compare to the levels of the DSD? Identical, wider, narrower?
2. You don't share the factors...so it's hard to know...but did you have raw material variation between the DSD and the full factorial? For example, a different batch from the two experiments might explain what you are seeing?
3. Did the same staff run the experiments? There might be operator variation.
4. How about the measurement system(s) for the responses? Did they change or do you even know the variation of these systems?
5. You use that dreaded word 'significance'. Some folks take a very strict view of 'significance' and use 'p - values' as a cliff to establish significance. Hopefully you aren't one of those folks...for example, these folks would say (presuming an 0.05 value is your 'cliff') that an effect whose p - value is 0.049 is significant, whilst another effect whose p - value is 0.051 is not significant. I'd argue both effects are worthy of further investigation. How do the p - values compare for consistent effects across the experiments.
6. How do the residuals compare using the model from the DSD to the actual results you observed in the full factorial? Are they practically useful/consistent...forgetting about p - values and such.
7. How does the responses vs. factor levels and experimental execution order compare across the experiments? Are they at least directionally consistent?
8. Lastly, can you share the results/data?