rounding off problem.....

I'm no expert in R internals or floating point computation, however, two things come to mind.

First, I suspect the exact value is stored. It is just the printing that looks rounded. That is likely because 0.001 completely dominates the rest. To print in full precision, you would need over 200 digits for some of your values.

Second, you may be pushing the limits of precision. It seems to me your original values are indistinguishable from zero. If they really represent materially different values, you might want to rescale them to improve computational reliability.