Have difficulty/difficulties (in) doing something

There is no real difference. The omission of prepositions in modifying phrases is and has been common in English:

He lived there [for] several years.

Kiplng L 108 I shall always be threepence short in my accounts = I shall always be short in my accounts by threepence

Gissing G 197 she blames herself no end = she blames herself without an end.

Darwin L 1.209 I can hardly think there will be a coronation [at] this time [in] fifty years.

Thus we have

keeping things - gerund phrase acting adjectivally

in keeping things - Adjectival prepositional modifier (in + gerund phrase.)

Examples taken from "A Modern English Grammar on Historical Principles Part7 Syntax V4 1949 by O Jespersen.