Scientists have determined that the inner ear assists in awareness of

Scientists have determined that the inner ear assists in awareness of body orientation, since people with disorders of the inner ear were found to have increased difficulties in maintaining balance.

Two problems tested:
1. verb tense
2. modifier/meaning

1. Simple past tense is typically used for events of the past that have definite time period: ..., in 1994 people with disorders of the inner ear were found to have increased difficulties in maintaining balance.
If definite time period is not specified, Present Perfect tense is preferred: ...orientation, since people with disorders of the inner ear have been found to have increased difficulty
Also, the usage of since and within in the context of time indicates the usage of present perfect (here since = because)

2.increased difficulties: increased correctly modifies difficulties and express that difficulties are already big
increasing difficulties: express a process that difficulties are continuously increasing in maintaining balance - distorts the meaning

(A) were found to have increased difficulties - have been found is preferable, since the event is not a point in a time event

(B) have been found to have increased difficulty - the best choice

(C) were found to have increasing difficulty - have been found is preferable, since the event is not a point in a time event + 'increased difficulties' is needed to maintain original meaning

(D) had been found to have increased difficulties - there is now verb tense had been found it is rather have been found

(E) have been found to have increasing difficulties - as discussed, 'increased difficulties' is needed to maintain original meaning