High Reconstruction Quality and Restart Repeatability Do Not Guarantee Recovery of Ground-Truth Muscle Synergies

High reconstruction quality and agreement across repeated fits do not necessarily establish recovery of muscle synergies. We tested whether a variance-accounted-for (VAF)/elbow rule recovers the generating synergy count and spatial vectors, whether high restart repeatability indicates recovery, and how five design factors affect recovery. Non-negative matrix factorisation was applied to 4,320 synthetic 16-muscle datasets varying generating rank, noise, trial count, spatial similarity and activation overlap. Combined recovery required the correct rank and cosine similarity of at least 0.80 for every matched spatial vector. Factor effects and two-factor interactions were assessed using exploratory heteroscedastic Wald tests with Benjamini-Hochberg adjustment. Rank selection was exact in 17.6% of datasets, too low in 54.9% and too high in 27.5%; combined recovery was 13.9%. Among fits with VAF at least 0.90, only 11.3% achieved combined recovery. Among 3,762 datasets with spatial repeatability at least 0.95, 19.6% had the correct rank and 15.7% achieved combined recovery. All five factors were associated with recovery (adjusted p < 0.001). Recovery declined from 26.2% to 1.7% with increasing spatial similarity and from 26.2% to 2.2% with increasing activation overlap. It was lower at ranks 7-9 than at 3-5, increased from 11.0% with 3 trials to 15.8% with 80 trials, and varied non-monotonically with noise. Five noiseless signals synthesised from measured-sEMG reference factors also showed under-selection despite VAF above 0.918. Under this selector, high reconstruction quality and restart agreement were insufficient indicators of correct rank and spatial recovery. Muscle-synergy interpretation should account for rank sensitivity and the separability of spatial and activation patterns.